Biogeographic regions and events of isolation and diversification of the endemic biota of the tropical Andes

Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae)

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.

The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?

Understanding how life history shapes genetic diversity is a fundamental issue in evolutionary biology, with important consequences for conservation. However, we still have an incomplete picture of the impact of life history on genome-wide patterns of diversity, especially in long-lived semelparous plants. Puya raimondii is a high-altitude semelparous species from the Andes that flowers at 40-100 years of age. We sequenced the whole genome and estimated the nucleotide diversity of 200 individuals sampled from nine populations. Coalescent-based approaches were then used to infer past population dynamics. Finally, these results were compared with results obtained for the iteroparous species, Puya macrura. The nine populations of P. raimondii were highly divergent, highly inbred, and carried an exceptionally high genetic load. They are genetically depauperate, although, locally in the genome, balancing selection contributed to the maintenance of genetic polymorphism. While both P. raimondii and P. macrura went through a severe bottleneck during the Pleistocene, P. raimondii did not recover from it and continuously declined, while P. macrura managed to bounce back. Our results demonstrate the importance of life history, in particular generation time and reproductive strategy, in affecting population dynamics and genomic variation, and illustrate the genetic fragility of long-lived semelparous plants.

Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands and landmasses, and indicates that Andean orogeny promotes speciation

The Neotropical region is the most diverse on the planet, largely owing to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to contribute to generating this diversity, including Andean orogeny, the closure of the Isthmus of Panama, the GAARlandia land bridge and historical connections among currently isolated forests. Micrathena spiders are diverse and widespread in the region, and thus a complete phylogeny of this genus allows the testing of hypotheses at multiple scales. We estimated a complete, dated phylogeny using morphological data for 117 Micrathena species and molecular data of up to five genes for a subset of 79 species. Employing event-based approaches and biogeographic stochastic mapping while considering phylogenetic uncertainty, we estimated ancestral distributions, the timing and direction of dispersal events and diversification rates among areas. The phylogeny is generally robust, with uncertainty in the position of some of the species lacking sequences. Micrathena started diversifying around 25 Ma. Andean cloud forests show the highest in-situ speciation, while the Amazon is the major dispersal source for adjacent areas. The Dry Diagonal generated few species and is a sink of diversity. Species exchange between Central and South America involved approximately 23 dispersal events and started ~20 Ma, which is consistent with a Miocene age for the Isthmus of Panama closure. We inferred four dispersal events from Central America to the Antilles in the last 20 Myr, indicating the spiders did not reach the islands through the GAARlandia land bridge. We identified important species exchange routes among the Amazon, Andean cloud forests and Atlantic forests during the Plio-Pleistocene. Sampling all species of the genus was fundamental to the conclusions above, especially in identifying the Andean forests as the area that generated the majority of species. This highlights the importance of complete taxonomic sampling in biogeographic studies.

Rethinking spatial history: envisioning a mechanistic historical biogeography

Historical biogeography is the study of geographic distributions of taxa through space and time. Over the last 50 years, several methods have been proposed to reconstruct these histories. However, despite their particularities, conceptually they have been most often derived from the reconstruction of area relationships. Here we advocate that area cladograms lack explanatory power and that biogeography needs to move towards a more mechanistic approach. We discuss the ontological problems related to areas of endemism and their validity as biogeographic units. Specifically, we propose that areas of endemism are not discrete historical entities and that area-based analyses are inappropriate for analytical biogeography. Instead, we suggest that biogeographic analyses should focus on those spatial-geographic elements that cause diversification, namely barriers. We discuss how barriers have more discrete boundaries in space and time than do areas of endemism, which allows the identification of homologous units and the recovery of vicariant events. Reconstructing the history of vicariant events results in a better understanding of spatial evolution within a biota because barrier formation is the relevant causal mechanism of diversification. We end by acknowledging the largely ignored views of Peter Hovenkamp and his conceptual contributions to developing a mechanistic biogeography.

Opportunity begets opportunity to drive macroevolutionary dynamics of a diverse lizard radiation

Evolution proceeds unevenly across the tree of life, with some lineages accumulating diversity more rapidly than others. Explaining this disparity is challenging as similar evolutionary triggers often do not result in analogous shifts across the tree, and similar shifts may reflect different evolutionary triggers. We used a combination of approaches to directly consider such context-dependency and untangle the complex network of processes that shape macroevolutionary dynamics, focusing on Pleurodonta, a diverse radiation of lizards. Our approach shows that some lineage-wide signatures are lost when conditioned on sublineages: while viviparity appears to accelerate diversification, its effect size is overestimated by its association with the Andean mountains. Conversely, some signals that erode at broader phylogenetic scales emerge at shallower ones. Mountains, in general, do not affect speciation rates; rather, the occurrence in the Andean mountains specifically promotes diversification. Likewise, the evolution of larger sizes catalyzes diversification rates, but only within certain ecological and geographical settings. We caution that conventional methods of fitting models to entire trees may mistakenly assign diversification heterogeneity to specific factors despite evidence against their plausibility. Our study takes a significant stride toward disentangling confounding factors and identifying plausible sources of ecological opportunities in the diversification of large evolutionary radiations.

Unveiling Colombia's medicinal Cannabis sativa treasure trove: Phenotypic and Chemotypic diversity in legal cultivation

INTRODUCTION

Cannabis sativa is a highly versatile plant with a long history of cultivation and domestication. It produces multiple compounds that exert distinct and valuable therapeutic effects by modulating diverse biological systems, including the endocannabinoid system (ECS). Access to standardized, metabolically diverse, and reproducible C. sativa chemotypes and chemovars is essential for physicians to optimize individualized patient treatment and for industries to conduct drug-discovery campaigns.

OBJECTIVE

This study aimed to characterize and assess the phytochemical diversity of C. sativa chemotypes in diverse ecological regions of Colombia, South America.

METHODOLOGY

Ten cannabinoids and 23 terpenes were measured using liquid and gas chromatography, in addition to other phenotypic traits, in 156 C. sativa plants that were grown in diverse ecological regions in Colombia, a hotspot for global biodiversity.

RESULTS

Our results reveal significant phytochemical diversity in Colombian-grown C. sativa plants, with four distinct chemotypes based on cannabinoid profile. The significant amount of usually uncommon terpenes suggests that Colombia's environments may have unique capabilities that allow the plant to express these compounds. Colombia's diverse climates offer enormous cultivation potential, making it a key player in both domestic and international medicinal and recreational C. sativa trade.

CONCLUSION

These findings underscore Colombia's capacity to pioneer global C. sativa production diversification, particularly in South America with new emerging markets.

Integrating niche and occupancy models to infer the distribution of an endemic fossorial snake (Atractus lasallei)

Understanding species distribution and habitat preferences is crucial for effective conservation strategies. However, the lack of information about population responses to environmental change at different scales hinders effective conservation measures. In this study, we estimate the potential and realized distribution of Atractus lasallei, a semi-fossorial snake endemic to the northwestern region of Colombia. We modelled the potential distribution of A. lasallei based on ecological niche theory (using maxent), and habitat use was characterized while accounting for imperfect detection using a single-season occupancy model. Our results suggest that A. lasallei selects areas characterized by slopes below 10°, with high average annual precipitation (>2500mm/year) and herbaceous and shrubby vegetation. Its potential distribution encompasses the northern Central Cordillera and two smaller centers along the Western Cordillera, but its habitat is heavily fragmented within this potential distribution. When the two models are combined, the species' realized distribution sums up to 935 km2, highlighting its vulnerability. We recommend approaches that focus on variability at different spatio-temporal scales to better comprehend the variables that affect species' ranges and identify threats to vulnerable species. Prompt actions are needed to protect herbaceous and shrub vegetation in this region, highly demanded for agriculture and cattle grazing.

Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus

The genus Pristimantis diversified in the tropical Andes mountains and is the most speciose genus of terrestrial vertebrates. Pristimantis are notable among frogs in that they thrive at high elevations (>2,000 m) and are direct developers without a tadpole stage. Despite their ecological significance, little is known about the genetic and physiological traits enabling their success. We conducted transcriptomic analysis on seven Pristimantis species sampled across elevations in the Ecuadorean Andes to explore three hypotheses for their success: (i) unique genes are under selection relative to all other frogs, (ii) common selection occurs across all direct developers, or (iii) common selection occurs across all high-elevation frog clades. Comparative analysis with 34 frog species revealed unique positive selection in Pristimantis genes related to aerobic respiration, hemostasis, signaling, cellular transportation of proteins and ions, and immunity. Additionally, we detected positive selection across all direct developers for genes associated with oxygenase activity and metal ion binding. While many genes under selection in Pristimantis were not positively selected in other high-elevation frog species, we identified some shared genes and pathways linked to lipid metabolism, innate immunity, and cellular redox processes. We observed more positive selection in duplicated- versus single-copy genes, while relaxed purifying selection was prevalent in single-copy genes. Notably, copy number of an innate immunity complement gene was positively correlated with Pristimantis species elevation. Our findings contribute novel insights into the genetic basis of adaptation in Pristimantis and provide a foundation for future studies on the evolutionary mechanisms leading to direct development and coping with high elevations.

Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana

Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non-genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central-peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation-with-gene-flow models generate the heterogeneous genome landscapes. These elements weight differently between central-island and other central-peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low-recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non-uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana.

Montane diversification as a mechanism of speciation in neotropical butterflies

The mountains in the Atlantic Forest domain are environments that harbor a high biodiversity, including species adapted to colder climates that were probably influenced by the climatic variations of the Pleistocene. To understand the phylogeographic pattern and assess the taxonomic boundaries between two sister montane species, a genomic study of the butterflies Actinote mantiqueira and A. alalia (Nymphalidae: Acraeini) was conducted. Analyses based on partial sequences of the mitochondrial gene COI (barcode region) failed to recover any phylogenetic or genetic structure discriminating the two species or sampling localities. However, single nucleotide polymorphisms gathered using Genotyping-by-Sequencing provided a strong isolation pattern in all analyses (genetic distance, phylogenetic hypothesis, clustering analyses, and F ST statistics) which is consistent with morphology, separating all individuals of A. alalia from all populations of A. mantiqueira. The three sampled mountain ranges where A. mantiqueira populations occur-Serra do Mar, Serra da Mantiqueira, and Poços de Caldas Plateau-were identified as three isolated clusters. Paleoclimate simulations indicate that both species' distributions changed according to climatic oscillations in the Pleistocene period, with the two species potentially occurring in areas of lower altitude during glacial periods when compared to the interglacial periods (as the present). Besides, a potential path between their distribution through the Serra do Mar Mountain range was inferred. Therefore, the Pleistocene climatic fluctuation had a significant impact on the speciation process between A. alalia and A. mantiqueira, which was brought on by isolation at different mountain summits during interglacial periods, as shown by the modeled historical distribution and the observed genetic structure.

Tectonic extension and paleoelevation influence mammalian diversity dynamics in the Basin and Range Province of western North America

Landscape properties have a profound influence on the diversity and distribution of biota, with present-day biodiversity hot spots occurring in topographically complex regions globally. Complex topography is created by tectonic processes and further shaped by interactions between climate and land-surface processes. These processes enrich diversity at the regional scale by promoting speciation and accommodating increased species richness along strong environmental gradients. Synthesis of the mammalian fossil record and a geophysical model of topographic evolution of the Basin and Range Province in western North America enable us to directly quantify relationships between mammal diversity and landscape dynamics over the past 30 million years. We analyze the covariation between tectonic history (extensional strain rates, paleotopography, and ruggedness), global temperature, and diversity dynamics. Mammal species richness and turnover exhibit stronger responses to rates of change in landscape properties than to the specific properties themselves, with peaks in diversity coinciding with high tectonic strain rates and large changes in elevation across spatial scales.

Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae)

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.

The role of biogeographical barriers on the historical dynamics of passerine birds with a circum-Amazonian distribution

Common distributional patterns have provided the foundations of our knowledge of Neotropical biogeography. A distinctive pattern is the "circum-Amazonian distribution", which surrounds Amazonia across the forested lowlands south and east of the basin, the Andean foothills, the Venezuelan Coastal Range, and the Tepuis. The underlying evolutionary and biogeographical mechanisms responsible for this widespread pattern of avian distribution have yet to be elucidated. Here, we test the effects of biogeographical barriers in four species in the passerine family Thamnophilidae by performing comparative demographic analyses of genome-scale data. Specifically, we used flanking regions of ultraconserved regions to estimate population historical parameters and genealogical trees and tested demographic models reflecting contrasting biogeographical scenarios explaining the circum-Amazonian distribution. We found that taxa with circum-Amazonian distribution have at least two main phylogeographical clusters: (1) Andes, often extending into Central America and the Tepuis; and (2) the remaining of their distribution. These clusters are connected through corridors along the Chaco-Cerrado and southeastern Amazonia, allowing gene flow between Andean and eastern South American populations. Demographic histories are consistent with Pleistocene climatic fluctuations having a strong influence on the diversification history of circum-Amazonian taxa, Refugia played a crucial role, enabling both phenotypic and genetic differentiation, yet maintaining substantial interconnectedness to keep considerable levels of gene flow during different dry/cool and warm/humid periods. Additionally, steep environmental gradients appear to play a critical role in maintaining both genetic and phenotypic structure.

An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates

AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.

Predicting the potential distribution of 12 threatened medicinal plants on the Qinghai-Tibet Plateau, with a maximum entropy model

Climate change is a vital driver of biodiversity patterns and species distributions, understanding how organisms respond to climate change will shed light on the conservation of endangered species. In this study, the MaxEnt model was used to predict the potential suitable area of 12 threatened medicinal plants in the QTP (Qinghai-Tibet Plateau) under the current and future (2050s, 2070s) three climate scenarios (RCP2.6, RCP4.5, RCP8.5). The results showed that the climatically suitable habitats for the threatened medicinal plants were primarily found in the eastern, southeast, southern, and some parts of the central regions on the QTP. Moreover, 25% of the threatened medicinal plants would have reduced suitable habitat areas within the next 30-50 years in the different future global warming scenarios. Among these medicinal plants, RT (Rheum tanguticum) would miss the most habitat (98.97%), while the RAN (Rhododendron anthopogonoides) would miss the least habitat (10.15%). Nevertheless, 33.3% of the threatened medicinal plants showed an increase in their future habitat area because of their physiological characteristics which are more adaptable to a wide range of climates. The climatic suitable habitat for 50% of the threatened medicinal plants would migrate to higher altitudes or higher latitudes regions. This study provides a data foundation for the conservation of biodiversity and wild medicinal plants on the QTP.

Evolutionary history of a cold-adapted limnephilid caddisfly: Effects of climate change and topography on genetic structure

The distribution of organisms is influenced by complex factors such as the phylogenetic evolutionary histories of species, the physiological and ecological characteristics of organisms, climate, and geographical and geohistorical features. In this study, we focused on a caddisfly, Asynarchus sachalinensis (Trichoptera: Limnephilidae), which has adapted to cold habitats. From phylogeographic analyses based on the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) and 16S rRNA regions and the nuclear DNA (nDNA) 18S rRNA, 28S rRNA, carbamoyl-phosphate synthetase (CAD), elongation factor-1 alpha (EF1-α), and RNA polymerase II (POLII) regions, two distinct genetic clades were detected. Clade I was shown to be widely distributed from Sakhalin to Honshu, whereas Clade II was only distributed within Honshu. The distributions of these clades overlapped in Honshu. The habitats were located at relatively lower altitudes for Clade I and higher altitudes for Clade II. The divergence time of these clades was estimated to be during the Pleistocene, indicating that repeated climatic changes facilitated distributional shifts. Haplotype network and demographic analyses based on the mtDNA COI region showed contrasting genetic structures in the two clades. It was indicated that the population sizes of Clade I had expanded rapidly in a recent period, whereas Clade II had maintained stable population sizes. The habitats of Clade II were typically isolated and scattered at high altitudes, resulting in restricted migration and dispersal because of their discontinuous "Sky Island" habitats. The habitats of Clade I were located at relatively low altitudes, and it was assumed that the populations were continuous, which resulted in a higher frequency of migration and dispersal between populations. Thus, differences in the spatial scale of the adapted habitats of each clade may have resulted in different patterns of population connectivity and fragmentation associated with repeated climatic changes during the Pleistocene. Our study provided new insight into the distributional patterns of cold-adapted aquatic insects in the Japanese Archipelago. Furthermore, the distributional shifts predicted by ecological niche modeling under future climatic change conditions were different for each clade. Therefore, different principles are required in the assessment of each clade to predict temporal changes in their distributions.

Idiosyncratic patterns of local species richness and turnover define global biodiversity hotspots

Tropical mountains are global biodiversity hotspots, owing to a combination of high local species richness and turnover in species composition. Typically, the highest local richness and turnover levels are implicitly assumed to converge in the same mountain regions, resulting in extraordinary species richness at regional to global scales. We investigated this untested assumption using high-resolution distribution data for all 9,788 bird species found in 134 mountain regions worldwide. Contrary to expectations, the mountain regions with the highest local richness differed from those with the highest species turnover. This finding reflects dissimilarities in the regions' climates and habitat compositions. Forest habitats and humid tropical climates characterize the mountain regions with the highest local richness. In contrast, mountain regions with the highest turnover are generally colder with drier climates and have mostly open habitat types. The highest local species richness and turnover levels globally converge in only a few mountain regions with the greatest climate volumes and topographic heterogeneity, resulting in the most prominent global hotspots for avian biodiversity. These results underline that species-richness hotspots in tropical mountains arise from idiosyncratic levels of local species richness and turnover, a pattern that traditional analyses of overall regional species richness do not detect.

Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China

The numerous naturally-fragmented sky islands (SIs) in the Hengduan Mountains Region (HMR) of southwestern China constitute discontinuous landscapes where montane habitats are isolated by dry-hot valleys which have fostered exceptional species diversification and endemicity. However, studies documenting the crucial role of SI on the speciation dynamics of native freshwater organisms are scarce. Here we used a novel set of comprehensive genetic markers (24 nuclear DNA sequences and complete mitogenomes), morphological characters, and biogeographical information to reveal the evolutionary history and speciation mechanisms of a group of small-bodied montane potamids in the genus Tenuipotamon. Our results provide a robustly supported phylogeny, and suggest that the vicariance events of these montane crabs correlate well with the emergence of SIs due to the uplift of the HMR during the Late Oligocene. Furthermore, ancestrally, mountain ridges provided corridors for the dispersal of these montane crabs that led to the colonization of moist montane-specific habitats, aided by past climatic conditions that were the crucial determinants of their evolutionary history. The present results illustrated that the mechanisms isolating SIs are reinforced by the harsh-dry isolating climatic features of dry-hot valleys separating SIs and continue to affect local diversification. This offers insights into the causes of the high biodiversity and endemism shown by the freshwater crabs of the HMR-SIs in southwestern China.

A new cryptic species of terrestrial breeding frog of the Pristimantisdanae Group (Anura, Strabomantidae) from montane forests in Ayacucho, Peru

Based on morphological and molecular characters, we describe a new species of terrestrial breeding frog of the Pristimantisdanae Group from montane forests of La Mar Province, Ayacucho Department in southern Peru, at elevations from 1200 to 2000 m a.s.l. The phylogenetic analysis, based on concatenated sequences of gene fragments of 16S rRNA, RAG1, COI and TYR suggests that the new species is a sister taxon of a clade that includes one undescribed species of Pristimantis from Cusco, Pristimantispharangobates and Pristimantisrhabdolaemus. The new species is most similar to P.rhabdolaemus, which differs by lacking scapular tubercules and by its smaller size (17.0-18.6 mm in males [n = 5], 20.8-25.2 mm in females [n = 5] in the new species vs. 22.8-26.3 mm in males [n = 19], 26.0-31.9 mm in females [n = 30] of P.rhabdolaemus). Additionally, we report the prevalence of Batrachochytriumdendrobatidis (Bd) in this species.

The Andean Ibis (Theristicus branickii) in South America: potential distribution, presence in protected areas and anthropic threats

The avifauna of South America is one of the most widely studied groups of vertebrates. However, certain species, such as the Andean Ibis (Theristicus branickii), have received limited attention regarding their ecological patterns, biology, current distribution, and environmental requirements. This study analyzed observation data from the Global Biodiversity Information Facility (GBIF) on the Andean Ibis in four countries to identify and understand critical variables that determine the species' presence, assess the proportion of its habitat within protected areas and identify possible threats to the species. Additionally, this study considered environmental and ecological variables to model ecological niches using the maximum entropy approach in MaxEnt to map the suitable habitat of the species. The findings revealed the extent of suitable Andean Ibis habitats in Ecuador, Peru, Bolivia and Chile. The variables that most determined the presence of the species were: altitude (36.57%), distance to lakes (23.29%) and ecological isothermality (13.34%). The distribution area of the Andean Ibis totaled 300,095.00 km2, spanning both sides of the Andean mountains range. Human activities have left a significant impact on the Andean Ibis habitat, with 48% of this area impacted by the human footprint and only 10% of the territory falling within protected areas designated by the respective countries. The results of this study show that the Andean Ibis presents characteristics of a specialist species due to its adaptation to the climate conditions of the plateau and highlands, including low temperatures, herbaceous vegetation and the presence of water bodies. The species is distributed in disconnected Andean landscape areas, whose functionality could be compromised by increased human activities. Complementary studies will be necessary to understand the ecological role and effectiveness of protected areas for conserving the species.

Is Eriocnemis luciani meridae (Aves: Trochilidae) a diagnosable taxon and does it come from Venezuela, with remarks on the collectors Salomn Briceo and Walther Frederick Henninger

Eriocnemis luciani meridae was originally described from a single specimen collected in the late 19th century in western Venezuela. Subsequently a second specimen of E. luciani, also labelled Venezuela, has been taken as additional proof for a highly disjunct population of this hummingbird, which otherwise ranges from southwest Colombia to southern Peru (taxonomy-dependent). Eriocnemis l. meridae has been accepted by all of the global checklists of birds, but has been routinely ignored by Venezuelan sources. In an effort to resolve this dichotomy of treatment, we re-examined the specimens plumage in comparison with relevant material in two major European bird collections. We found that the characters used to erect E. l. meridae are only doubtfully or weakly expressed in the holotype and appear invisible in the Ohio specimen, but both are clearly referrable to the species E. luciani. Evidence that the second specimen was definitely collected in Venezuela is weak and its overall provenance is unclear. In contrast, an extensive historical investigation of the relevant collectors indicates that the holotype does appear to have been taken in Venezuela, although perhaps not in the precise locality indicated for it. This leaves an unusual situation whereby we consider the case for a separate Venezuelan endemic taxon to be unproven, but there is no incontrovertible reason to exclude the species from the countrys avifauna; according to recent niche modelling data it is best searched for in the Sierra Nevada of Mrida state. In contrast, a second subspecies of E. luciani, E. l. baptistae, described by the same authors as endemic to part of western Ecuador is, according to our reappraisal, clearly diagnosable and is upheld.

Ancient allopatry and ecological divergence act together to promote plant diversity in mountainous regions: evidence from comparative phylogeography of two genera in the Sino-Himalayan region

BACKGROUND

How geographical isolation and ecological divergence act together to promote plant diversity in mountainous regions remains largely unknown. In this study, we chose two genera comprising a small number of species distributed in the Sino-Himalayan region, Megacodon (Gentianaceae) and Beesia (Ranunculaceae), which both exhibit a fragmented distribution pattern and are found across a wide range of elevations. By summarizing their common patterns of speciation and/or divergence processes, we aim to understand how environmental changes accelerated lineage diversification in the Sino-Himalayan region through ancient allopatry and ecological divergence.

RESULTS

Using ddRAD-seq, chloroplast genome sequences, and specific molecular markers, we studied the phylogenetic relationships, population structure, and historical biogeography of Beesia and Megacodon. Both genera began to diverge from the late Miocene onwards, with ancient allopatry at lower elevations formed narrow-range species or relict populations. Mantel tests between genetic distance and climatic, elevational, or geographic distance revealed an isolation-by-distance pattern in Beesia and Megacodon stylophorus. Megacodon showed two clades occupying entirely different altitudinal ranges, whereas Beesia calthifolia exhibited a genetic divergence pattern along an elevation gradient. Furthermore, we conducted morphological measurements on Beesia calthifolia and found that different elevational groups had distinct leaf shapes.

CONCLUSIONS

The regional disjunctions of plant groups in the Sino-Himalayan region are drastic and closely related to several biogeographic boundaries. As a consequence of major geological and climate change, ecological divergence when different elevations are colonized often happens simultaneously within plant groups. Although habitat fragmentation and parapatric ecological divergence each spur speciation to different extents, a combined effect of these two factors is a common phenomenon in the Sino-Himalayan region.

Unraveling plant-pollinator interactions from a south-west Andean forest in Colombia

Background

Loss of biological connectivity increases the vulnerability of ecological dynamics, thereby affecting processes such as pollination. Therefore, it is important to understand the roles of the actors that participate in these interaction networks. Nonetheless, there is a significant oversight regarding the main actors in the pollination networks within the highly biodiverse forests of Colombia. Hence, the present study aims to evaluate the interaction patterns of a network of potential pollinators that inhabit an Andean Forest in Totoró, Cauca, Colombia.

Methods

The interactions between plants and potential pollinators were recorded through direct observation in 10 transects during six field trips conducted over the course of one year. Subsequently, an interaction matrix was developed, and network metrics such as connectance, specialization, nestedness, and asymmetry of interaction strength were evaluated by applying null models. An interpolation/extrapolation curve was calculated in order to assess the representativeness of the sample. Finally, the key species of the network were identified by considering degree (k), centrality, and betweenness centrality.

Results

A total of 53 plant species and 52 potential pollinator species (including insects and birds) were recorded, with a sample coverage of 88.5%. Connectance (C = 0.19) and specialization (H2' = 0.19) were low, indicating a generalist network. Freziera canescens, Gaiadendron punctatum, Persea mutisii, Bombus rubicundus, Heliangelus exortis, Chironomus sp., and Metallura tyrianthina were identified as the key species that contribute to a more cohesive network structure.

Discussion

The present study characterized the structure of the plant-pollinator network in a highly diverse Andean forest in Colombia. It is evident that insects are the largest group of pollinators; however, it is interesting to note that birds form a different module that specializes in pollinating a specific group of plants. On the other hand, the diversity and generality of the species found suggest that the network may be robust against chains of extinction. Nevertheless, the presence of certain introduced species, such as Apis mellifera, and the rapid changes in vegetation cover may affect the dynamics of this mutualistic network. So, it is imperative to apply restoration and conservation strategies to these ecosystems in order to enhance plant-animal interactions and prevent the loss of taxonomical and functional diversity.

Empirical delineation of the forest-steppe zone is supported by macroclimate

Eurasian forest-steppes form a 9000-km-long transitional zone between temperate forests and steppes, featuring a complex mosaic of herbaceous and woody habitats. Due to its heterogeneity regarding climate, topography and vegetation, the forest-steppe zone has been divided into several regions. However, a continental-scale empirical delineation of the zone and its regions was missing until recently. Finally, a map has been proposed by Erdős et al. based on floristic composition, physiognomy, relief, and climate. By conducting predictive distribution modeling and hierarchical clustering, here we compared this expert delineation with the solely macroclimate-based predictions and clusters. By assessing the discrepancies, we located the areas where refinement of the delineation or the inclusion of non-macroclimatic predictors should be considered. Also, we identified the most important variables for predicting the existence of the Eurasian forest-steppe zone and its regions. The predicted probability of forest-steppe occurrence showed a very high agreement with the expert delineation. The previous delineation of the West Siberia region was confirmed by our results, while that of the Inner Asia region was the one least confirmed by the macroclimate-based model predictions. The appropriate delineation of the Southeast Europe region from the East Europe region should be refined by further research, and splitting the Far East region into a southern and northern subregion should also be considered. The main macroclimatic predictors of the potential distribution of the zone and its regions were potential evapotranspiration (zone and regions), annual mean temperature (regions), precipitation of driest quarter (regions) and precipitation of warmest quarter (zone), but the importance of climatic variables for prediction showed great variability among the fitted predictive distribution models.

An updated checklist of the wild silkmoths (Lepidoptera, Saturniidae) of Colombia

In recent years, the study of wild silkmoths (Lepidoptera: Saturniidae) has increased exponentially due to the intense sampling effort and the use of molecular evidence for species delimitation, which led to the description of numerous new taxa especially from the Neotropic. Given these rapid advances, the checklist of the Colombian Saturniidae needs to be updated to cover the taxonomy, distribution, and diversity of these moths in the country. After an extensive review of literature, data repositories, and collections, an updated and comprehensive list of Saturniidae from Colombia is presented, including their occurrence status in each Colombian department. The checklist includes 7 subfamilies, 55 genera, and 790 taxa (766 in species rank) of Saturniidae in Colombia. Current distribution data show that the genus Winbrechlinia, the subgenusDarylesia, 379 species, and 18 subspecies are endemic to Colombia. Moreover, a dichotomic key to the Colombian subfamilies is provided. A few taxonomic changes are proposed based on a thorough taxonomic revision of the Colombian taxa. This revision also addresses the issue of outdated species names reported in the first checklist of Colombian Saturniidae (Amarillo-Suárez 2000) and excludes old records of taxa that are considered dubious for Colombia based on new evidence. By presenting an updated list of Colombian species, including the newly described taxa, this study aims at eliminating confusion stemming from outdated names and provides a useful resource for researching and conservating Saturniidae in Colombia. We wish to offer a common reference for future studies on the biodiversity and biogeography of moths in the Neotropical realm.

What Darwin could not see: island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species

Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.

Testing Geology with Biology: Plate Tectonics and the Diversification of Microhylid Frogs in the Papuan Region

Studies of the Papuan region have provided fundamental insights into the evolutionary processes generating its exceptional biodiversity, but the influence of geological processes merits further study. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization and island archipelagos with varying degrees of isolation promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories. Asterophryine frogs are a hyperdiverse clade representing half the world's microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history explains this far and wide distribution of a clade that should have poor dispersal abilities. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly supports an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Range on the EPCT, and the recent proximity of the large New Britain Island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across large ocean barriers to the offshore islands, against the predictions of island biogeography theory, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, changing in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.

Systematics and biogeography of Anoura cultrata (Mammalia, Chiroptera, Phyllostomidae): a morphometric, niche modeling, and genetic perspective, with a taxonomic reappraisal of the genus

The nectar-feeding bats of the genus Anoura are widely distributed in the Neotropics, but are most speciose in the Andes. Anoura cultrata is a rare mid-elevation bat occurring in South and Central America. It is thought to be one of the few bat species exemplifying a latitudinal cline in body size. We address three systematic and biogeographic questions: 1) is the geographic variation in A. cultrata continuous, as argued to justify its current monotypic status? 2) do ecogeographic barriers to dispersal affect such variation? and 3) how do the genetic divergence and biogeography of the species compare to those of other members of the genus? To answer these questions, we used morphometric analyses, ecological niche modeling, and DNA barcoding. We divided the samples of A. cultrata into six geographic groups, delimited by topographic depressions separating mountain systems. We did not find significant correlations between body size and the geographic coordinates within five groups. Therefore, we conclude that ecogeographic barriers to dispersal between the regions occupied by such groups influenced morphometric variation in A. cultrata, and that despite its general north to south reduction in body size, the species does not show continuous clinal variation. A recent phylogenetic study of the genus Anoura concluded that it contains seven valid species. Our DNA barcoding analysis and morphological examination indicated that at least 10 species should be recognized, including A. peruana distinct from A. geoffroyi, and A. aequatoris and A. luismanueli distinct from A. caudifer. Moreover, we show that Central and South American populations of A. cultrata differ from each other at least at the subspecific level, thus we respectively refer to them as A. cultrata cultrata and as A. c. brevirostrum. Similarly, we refer to Central American and Mexican populations of 'A. geoffroyi' as A. peruana lasiopyga, and to their South American counterparts as A. p. peruana. The range of the latter subspecies reaches northeastern Venezuela. The Andes from southern Colombia to northern Peru appear to be the ancestral range of the genus.

A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean Grasslands

We describe a new terrestrial frog from the puna grasslands adjacent to the Mantaro dry valley in southern Peru. Phrynopus apumantarumsp. nov. is similar in appearence to P. bufoides but is differentiable by lacking discoidal fold and enlarged warts on dorsum, lacking a prominent post ocular fold and having canthal and post ocular stripe. Lastly, we propose to place the new species under the Vulnerable (VU) category of the IUCN Red List, due its small distribution and habitat loss recorded at the type locality.

The importance of the Andes in the evolutionary radiation of Sigmodontinae (Rodentia, Cricetidae), the most diverse group of mammals in the Neotropics

The Andean mountains stand out for their striking species richness and endemicity that characterize many emblematic Neotropical clades distributed in or around these mountains. The radiation of the Sigmodontinae subfamily, the most diversified mammalian group in the Neotropics, has been historically related to Andean orogenesis. We aim to evaluate this interplay between geological processes and biological responses through the diversification dynamics, the biogeographical history, and the range evolution of the subfamily. For these, we built the most comprehensive phylogeny and gathered 14,836 occurrences for the subfamily. We identified one shift in the speciation rate in the genus Akodon, which suffered their Andean radiation after the arrival of non-Andean ancestors. Our biogeographic analyses show multiple dispersal paths throughout the evolution that allowed this subfamily to colonize all Neotropics. The Northern Andes and Central-Southern Andes were the most important sources of diversity. In addition, the Central-Southern Andes were the most relevant sink, receiving the highest number of lineages. The Andean region exhibited higher speciation and turnover rates than non-Andean regions. Thus, our results support the crucial role of the Andean Mountains in the Sigmodontinae radiation, acting as a "macroevolutionary cradle" and "species attractor" for several sigmodontine lineages at different times, and as a "species pump" becoming the biogeographic source of multiple widely distributed neotropical lineages. Then, complex macroevolutionary dynamics would explain these rodents' high extant Andean diversity and their wide distribution in the Neotropics.

Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake

Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 --N and NO3 --N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.

The complete chloroplast genome sequences of three Broussonetia species and comparative analysis within the Moraceae

Background

Species of Broussonetia (family Moraceae) are commonly used to make textiles and high-grade paper. The distribution of Broussonetia papyrifera L. is considered to be related to the spread and location of humans. The complete chloroplast (cp) genomes of B. papyrifera, Broussonetia kazinoki Sieb., and Broussonetia kaempferi Sieb. were analyzed to better understand the status and evolutionary biology of the genus Broussonetia.

Methods

The cp genomes were assembled and characterized using SOAPdenovo2 and DOGMA. Phylogenetic and molecular dating analysis were performed using the concatenated nucleotide sequences of 35 species in the Moraceae family and were based on 66 protein-coding genes (PCGs). An analysis of the sequence divergence (pi) of each PCG among the 35 cp genomes was conducted using DnaSP v6. Codon usage indices were calculated using the CodonW program.

Results

All three cp genomes had the typical land plant quadripartite structure, ranging in size from 160,239 bp to 160,841 bp. The ribosomal protein L22 gene (RPL22) was either incomplete or missing in all three Broussonetia species. Phylogenetic analysis revealed two clades. Clade 1 included Morus and Artocarpus, whereas clade 2 included the other seven genera. Malaisia scandens Lour. was clustered within the genus Broussonetia. The differentiation of Broussonetia was estimated to have taken place 26 million years ago. The PCGs' pi values ranged from 0.0005 to 0.0419, indicating small differences within the Moraceae family. The distribution of most of the genes in the effective number of codons plot (ENc-plot) fell on or near the trend line; the slopes of the trend line of neutrality plots were within the range of 0.0363-0.171. These results will facilitate the identification, taxonomy, and utilization of the Broussonetia species and further the evolutionary studies of the Moraceae family.

Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases

Biomes are climatically and biotically distinctive macroecological units that formed over geological time scales. Their features consolidate them as ‘evolutionary scenarios’, with their own diversification dynamics. Under the concept of phylogenetic niche conservatism, we assessed, for the first time, the evolution of biome occupation in birds. We aimed to analyse patterns of adaptation to different climatic regimes and the determinant factors for colonization of emerging biomes by clades from different ancestral biomes. In this work, we reconstructed the biome occupation history of two clades of birds (Galliformes and Falconiformes) under an integrative perspective through a comprehensive review of ecological, phylogenetic, palaeontological and biogeographical evidence. Our findings for both groups are consistent with a scenario of phylogenetic biome conservatism and highlight the importance of changes in climate during the Miocene in the adaptation and evolution of climatic niches. In particular, our results indicate high biome conservatism associated with biomes situated in some of the extremes of the global climate gradient (evergreen tropical rainforest, steppe and tundra) for both bird taxa. Finally, the historical dynamics of tropical seasonal biomes, such as tropical deciduous woodlands and savannas, appear to have played a preponderant role during the diversification processes of these bird lineages.

Genomic analyses of the scorpion mud turtle (Kinosternon scorpioides) (Linnaeus, 1766) in insular and continental Colombia: Evidence for multiple conservation and taxonomic units

The turtle genus Kinosternon is widespread with at least 25 species distributed from Mexico to northern Argentina. The taxonomy of this genus is controversial and requires a full revision using both morphological and molecular approaches. In this study, we did a genomic analysis on the species Kinosternon scorpioides distributed in insular and continental Colombia in order to define conservation units. Total DNA was extracted from 24 tissue samples and RADseq genotyping analysis was done. In addition, the intron R35 was amplified and sequenced for a subset of samples. A total of 35,507 SNPs combined with 1,047 bp of the intron were used for spatiotemporal colonization pattern reconstruction and phylogenetic analyses. In addition, SNPs were used for population structure inferences and allele frequency-based analyses. Reciprocal monophyly, significant differences in allele frequencies (Fst = 0.32 - 0.78), and evidence of reproductive isolation (no admixture/geneflow), indicate long-term divergence between groups (2-8 MYA), possibly due to geographical barriers. Four Evolutionarily Significant Units (ESUs) were defined within our samples. One ESU was represented by the insular subspecies K. scorpioides albogulare, found on San Andrés island, and three ESUs were defined for the subspecies K. s. scorpioides in continental Colombia: one trans-Andean, found in northwestern Colombia (Caribbean region) and two cis-Andean, found in eastern and southeastern Colombia in the Orinoco and Amazon regions, respectively. Colonization of this species occurred from an ancestral area on South of Central America region (~ 8.43 MYA), followed by an establishing of current populations on San Andrés Island and then, in the continent. First, in the Colombian Caribbean, next, in the Orinoco, and more recently, in the Amazon. We hypothesize that the emergence of the Panamá Isthmus, as well as the final uplift of the North Eastern Andes and Vaupes Arch, were key event leading to the differentiation of these ESUs. For management and conservation purposes, each of these ESUs should be considered as a separate management unit. A full revision of the taxonomy of the genus Kinosternon is warranted.

Biodiversity cradles and museums segregating within hotspots of endemism

The immense concentrations of vertebrate species in tropical mountains remain a prominent but unexplained pattern in biogeography. A long-standing hypothesis suggests that montane biodiversity hotspots result from endemic species aggregating within ecologically stable localities. Here, the persistence of ancient lineages coincides with frequent speciation events, making such areas both 'cradles' (where new species arise) and 'museums' (where old species survive). Although this hypothesis refers to processes operating at the scale of valleys, it remains supported primarily by patterns generated from coarse-scale distribution data. Using high-resolution occurrence and phylogenetic data on Andean hummingbirds, we find that old and young endemic species are not spatially aggregated. The young endemic species tend to have non-overlapping distributions scattered along the Andean treeline, a long and narrow habitat where populations easily become fragmented. By contrast, the old endemic species have more aggregated distributions, but mainly within pockets of cloud forests at lower elevations than the young endemic species. These findings contradict the premise that biogeographical cradles and museums should overlap in valley systems where pockets of stable climate persist through periods of climate change. Instead, Andean biodiversity hotspots may derive from large-scale fluctuating climate complexity in conjunction with local-scale variability in available area and habitat connectivity.

The tribe Dysoniini part VI: Phylogeny, biogeography and evolutionary trends of the lichen katydid genera (Orthoptera: Tettigoniidae: Phaneropterinae). Eleventh contribution to the suprageneric organization of Neotropical phaneropterines

The tribe Dysoniini is widely distributed in the Neotropics, ranging from northeastern Mexico across Central and South America to northern Argentina. In the latter subcontinent it is most diverse. These tettigoniids are remarkable for their lichen- and bryophyte-mimicking camouflage and for having a particularly elevated vertex, which is unusual in the family Phaneropterinae.                 A cladistic analysis for 23 terminal taxa has been performed (20 in the ingroup and 3 in the outgroup), using 76 morphological and ecological characters in order to prove monophyly of the following genera and tribes: Hammatoferina n. subtr. (including Hammatofera), Markiina n. subtr. (Machimoides (Machima (Apolinaria (Lichenodraculus + Markia)))) and Dysoniina n. stat. (Quiva (Yungasacris (Dissonulichen (Alexanderellus n. gen. (Paraphidnia + Anaphidna) (Dysonia (Lichenomorphus + Lichenodentix)))))). The tribe’s genera resulted as monophyletic, except for Dysonia sensu Gorochov, so it was necessary to revalidate generic status for Dissonulichen n. stat. to recover monophyly for Dysonia. The three aforementioned subtribes and a new subgenus Dissonulichospinus n. subgen. (within Dissonulichen n. stat.) are proposed, as well as five new combinations of species so far included in Dysonia: Alexanderellus mariposa n. comb., Dissonulichen diffusus n. comb., D. ornatus n. comb., D. elegans n. comb. and Lichenomorphus pirani n. comb. Four species names are considered as synonyms: Hammatofera brasiliensis n. syn. (under H. nodicornis), Dysonia similis n. syn. (under Dissonulichen minensis), Dysonia cuiabensis n. syn. (under Dissonulichen hebardi) and Lichenomorphus nigriventer n. syn. (under L. puntifrons). Dysonia lamellipes is considered a nomen dubium.                 Characters referring to camouflage, mimicry, and behaviors associated with these adaptative preferences were optimized. Optimizations for structural phylogenies were indicated on each of the optimized characters, displaying nodes in which the different optimizations by characters differ. Characters analyzed on the ambulatory behavior of the studied taxa are closely related to the type of mimicry or camouflage occurring in each group, so those taxa that camouflage in foliose lichen move in a slow, circumspect fashion, contrasting to taxa mimicking crustose or fruticose lichen, which simulate lichen parts stirred by a breeze. This most effective strategy makes them almost impossible to spot in their natural habitat. Likewise, species with wasp mimicry tend to show behaviors that make their imitation strategy more efficient. The ancestral state of the tribe is a phyllomorphic type (leaf camouflage) as is usual in most genera of the family Phaneropterinae. The appearance of camouflage and mimicry in the species of the tribe is discussed, and how these converge with taxa of other areas of the planet. The relationship between optimized characters is then grouped in the most parsimonious tree, indicating frequency and relation between taxa and characters.                 A biogeographic dispersal-vicariance analysis of the tribe’s genera indicates that the ancestral area is in the Brazilian Shield as the only resulting ancestral distribution, with a secondary center of radiation in the Andes. Four vicariant events are postulated: 1) The differentiation of some genera by the rising of the Andes, 2) forming a barrier between species groups of the genus Markia. 3) Expansion from the ancestral area towards the Amazon and 4) the Andes. Diagnoses and a pictorial key to the identification of all genera, plus conventional keys for identification of all species are provided, along with distribution maps. A list presents all taxa of the tribe within the proposed classification, including distribution data, depositories of type specimens, and additional comments.  

The Tracking of Moist Habitats Allowed Aiphanes (Arecaceae) to Cover the Elevation Gradient of the Northern Andes

The topographic gradients of the Tropical Andes may have triggered species divergence by different mechanisms. Topography separates species' geographical ranges and offers climatic heterogeneity, which could potentially foster local adaptation to specific climatic conditions and result in narrowly distributed endemic species. Such a pattern is found in the Andean centered palm genus Aiphanes. To test the extent to which geographic barriers and climatic heterogeneity can explain distribution patterns in Aiphanes, we sampled 34 out of 36 currently recognized species in that genus and sequenced them by Sanger sequencing and/or sequence target capture sequencing. We generated Bayesian, likelihood, and species-tree phylogenies, with which we explored climatic trait evolution from current climatic occupation. We also estimated species distribution models to test the relative roles of geographical and climatic divergence in their evolution. We found that Aiphanes originated in the Miocene in Andean environments and possibly in mid-elevation habitats. Diversification is related to the occupation of the adjacent high and low elevation habitats tracking high annual precipitation and low precipitation seasonality (moist habitats). Different species in different clades repeatedly occupy all the different temperatures offered by the elevation gradient from 0 to 3,000 m in different geographically isolated areas. A pattern of conserved adaptation to moist environments is consistent among the clades. Our results stress the evolutionary roles of niche truncation of wide thermal tolerance by physical range fragmentation, coupled with water-related niche conservatism, to colonize the topographic gradient.

Extinction, coextinction and colonization dynamics in plant-hummingbird networks under climate change

Climate-driven range shifts may cause local extinctions, while the accompanying loss of biotic interactions may trigger secondary coextinctions. At the same time, climate change may facilitate colonizations from regional source pools, balancing out local species loss. At present, how these extinction-coextinction-colonization dynamics affect biological communities under climate change is poorly understood. Using 84 communities of interacting plants and hummingbirds, we simulated patterns in climate-driven extinctions, coextinctions and colonizations under future climate change scenarios. Our simulations showed clear geographic discrepancies in the communities' vulnerability to climate change. Andean communities were the least affected by future climate change, as they experienced few climate-driven extinctions and coextinctions while having the highest colonization potential. In North America and lowland South America, communities had many climate-driven extinctions and few colonization events. Meanwhile, the pattern of coextinction was highly dependent on the configuration of networks formed by interacting hummingbirds and plants. Notably, North American communities experienced proportionally fewer coextinctions than other regions because climate-driven extinctions here primarily affected species with peripheral network roles. Moreover, coextinctions generally decreased in communities where species have few overlapping interactions, that is, communities with more complementary specialized and modular networks. Together, these results highlight that we should not expect colonizations to adequately balance out local extinctions in the most vulnerable ecoregions.

Phylogenetic relationships and evolutionary patterns of the genus Psammolestes Bergroth, 1911 (Hemiptera: Reduviidae: Triatominae)

BACKGROUND

The evolutionary history of biodiversity in South America has been poorly studied in the seasonal dry tropical forest (SDTF). Species diversification in this ecosystem may have a twofold explanation. First, intermittent connections in the middle and late Pleistocene promoted species dispersal and/or genetic connectivity between lineages isolated in disjunct patches of forest. Second, allopatric speciation proceeded immediately after the formation and colonization of the SDTF in the Neogene. Here we studied the diversification of Psammolestes, a genus endemic of the SDTF and naturally infected with Trypanosoma cruzi (agent of Chagas disease), using a combination of phylogenetic, population genetics and niche model methods, and evaluated the reliability of the three morphospecies currently recognized.

RESULTS

Our multilocus analyses recovered P. coreodes and P. tertius in a monophyletic clade sister to P. arthuri. Species delimitation tests recovered these lineages as different species despite the shared genetic variation observed between P. coreodes and P. tertius in five genes. Also, genetic variation of the genus clustered in three groups that were consistent with the three morphospecies. Our demographic model predicted a scenario of divergence in absence of gene flow, suggesting that mixed haplotypes may be the result of shared ancestral variation since the divergence of the subtropical-temperate species P. coreodes and P. tertius. In contrast, the tropical species P. arthuri was highly differentiated from the other two in all tests of genetic structure, and consistently, the Monmonier's algorithm identified a clear geographical barrier that separates this species from P. coreodes and P. tertius.

CONCLUSIONS

We found three genetically structured lineages within Psammolestes that diverged in absence of gene flow in the late Miocene. This result supports a scenario of species formation driven by geographical isolation rather than by divergence in the face of gene flow associated with climatic oscillations in the Pleistocene. Also, we identified the Amazon basin as a climatic barrier that separates tropical from subtropical-temperate species, thus promoting allopatric speciation after long range dispersion. Finally, each species of Psammolestes occupies different climatic niches suggesting that niche conservatism is not crucial for species differentiation. These findings influence the current vector surveillance programs of Chagas disease in the region.

Patterns of genomic divergence in sympatric and allopatric speciation of three Mihoutao (Actinidia) species

Isolation by geographic distance is involved in the formation of potential genomic islands and the divergence of genomes, which often result in speciation. The mechanisms of sympatric and allopatric speciation associated with geographic distance remain a topic of interest to evolutionary biologists. Here, we examined genomic divergence in three Actinidia species from large-scale sympatric and allopatric regions. Genome sequence data revealed that hexaploid Actinidia deliciosa originated from Actinidia chinensis and supported the speciation-with-gene-flow model in sympatric regions. The common ancestor of Actinidia setosa and A. deliciosa migrated from the mainland to the Taiwan Island ~2.91 Mya and formed A. setosa ~0.92 Mya, and the speciation of A. setosa is consistent with the divergence-after-speciation model with selective sweeps. Geographic isolation resulted in population contraction and accelerated the process of lineage sorting and speciation due to natural selection. Genomic islands contained genes associated with organ development, local adaptation, and stress resistance, indicating selective sweeps on a specific set of traits. Our results highlight the patterns of genomic divergence in sympatric and allopatric speciation, with the mediation of geographic isolation in the formation of genomic islands during Actinidia speciation.

Stink bugs (Hemiptera: Heteroptera: Pentatomidae) of Colombia: An annotated checklist of species

A checklist of 5 subfamilies, 108 genera, and 246 species of stinks bugs (Hemiptera, Pentatomidae) from Colombia is provided. Three genera [Andrallus Bergroth, Placocoris Mayr, and Pseudobebaeus Distant], and eight species [Arocera spectabilis (Drury), Andrallus spinidens (Fabricius), Banasa excavata Thomas, Banasa saileri Thomas, Banasa varians Stål, Chinavia scutellata (Distant), Pelidnocoris haglundi Ruckes, and Pseudobebaeus truncatus (Fallou)] are recorded for the first time from Colombia. Images of dorsal external habitus for all genera that occur in Colombia are offered. This is the first time a comprehensive list of the stink bugs from Colombia is presented, providing a baseline to develop further studies in this group of true bugs.  

Landscape Evolution as a Diversification Driver in Freshwater Fishes

The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with &gt; 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (&lt;0.5%) or total aquatic habitat volume (&lt;0.001%). This study asks if the fish species richness of the world’s river basins is explainable in terms of river captures using topographic metrics as proxies. The River Capture Hypothesis posits that drainage-network rearrangements have accelerated biotic diversification through their combined effects on dispersal, speciation, and extinction. Yet rates of river capture are poorly constrained at the basin scale worldwide. Here we assess correlations between fish species density (data for 14,953 obligate freshwater fish species) and basin-wide metrics of landscape evolution (data for 3,119 river basins), including: topography (elevation, average relief, slope, drainage area) and climate (average rainfall and air temperature). We assess the results in the context of both static landscapes (e.g., species-area and habitat heterogeneity relationships) and transient landscapes (e.g., river capture, tectonic activity, landscape disequilibrium). We also relax assumptions of functional neutrality of basins (tropical vs. extratropical, tectonically stable vs. active terrains). We found a disproportionate number of freshwater species in large, lowland river basins of tropical South America, Africa, and Southeast Asia, under predictable conditions of large geographic area, tropical climate, low topographic relief, and high habitat volume (i.e., high rainfall rates). However, our results show that these conditions are only necessary, but not fully sufficient, to explain the basins with the highest diversity. Basins with highest diversity are all located on tectonically stable regions, places where river capture is predicted to be most conducive to the formation of high fish species richness over evolutionary timescales. Our results are consistent with predictions of several landscape evolution models, including the River Capture Hypothesis, Mega Capture Hypothesis, and Intermediate Capture Rate Hypothesis, and support conclusions of numerical modeling studies indicating landscape transience as a mechanistic driver of net diversification in riverine and riparian organisms with widespread continental distributions.

Divergence times of the Rhoadsia clade (Characiformes: Characidae)

Abstract The family Characidae is the most diverse group of fishes in the Neotropics with challenging systematics. The three genera Carlana, Parastremma, and Rhoadsia, formerly considered the subfamily Rhoadsiinae, are now included in the subfamily Stethaprioninae. Previous phylogenetic analyses did not include all genera of Rhoadsiinae, specifically Parastremma. Here, we estimated the phylogenetic relationships and divergence times of the genera of Rhoadsiinae (the Rhoadsia clade) relative to the most representative genera of the Characidae. We used six molecular markers from the mitochondrial and nuclear genome to estimate the phylogeny and divergence times. We confirmed the monophyly of the Rhoadsia clade. Furthermore, we estimated that the Central American genus Carlana and the western Colombian genus Parastremma diverged approximately 13 Mya (95% HPD 8.36–18.11), consistent with the early-closure estimates of the Isthmus of Panama (~15 Mya). The genus Rhoadsia, endemic to Western Ecuador and Northern Peru, was estimated to originate at around 20 Mya (95% HPD 14.35–25.43), consistent with the Andean uplift (~20 Mya).

Community modeling reveals the importance of elevation and land cover in shaping migratory bird abundance in the Andes

The tropical Andes are characterized by extreme topographic and climatic complexity, which has likely contributed to their outstanding current species diversity, composed of many range-restricted species. However, little is known about how the distribution and abundance of highly mobile organisms, like long-distance migratory birds, varies across different land covers, elevations, and climatic conditions within the Andes. We conducted 1,606 distance-sampling point counts across the Colombian Andes, spanning elevations from 253 to 3,708 m, a range of precipitation regimes and representative land covers. We then employed a novel application of a multispecies hierarchical modeling approach to evaluate how elevation, local land cover, aboveground woody biomass, cloud cover, precipitation, and seasonality in precipitation shape the abundance of the migratory land bird community in the Andes. We detected 1,824 individuals of 29 species of migratory land birds, six of which were considered incidental in our study region. We modeled the abundance of the remaining 23 species, while considering observer and time of day effects on detectability. We found that both elevation and land cover had an overriding influence on the abundance of migratory species across the Andes, with strong evidence for a mid-elevation peak in abundance, and species-specific responses to both variables. As a community, migratory birds had the highest mean abundance in shade coffee plantations, secondary forest, and mature forest. Aboveground woody biomass did not affect the abundance of all species as a group, but a few showed strong responses to this variable. Contrary to predictions of a positive correlation between abundance and precipitation, we found no evidence for community-level responses to precipitation, aside for a weak tendency for birds to select areas with intermediate levels of precipitation. This novel use of a multispecies model sheds new light on the mechanisms shaping the winter distribution of migratory birds and highlights the importance of elevation and land cover types over climatic variables in the context of the Colombian Andes.