Isolation by resistance explains genetic diversity in the Arremon brushfinches of northern Mesoamerica.

Genetic differentiation between and within natural populations is the result of the joint effects of neutral and adaptative processes. In addition, the spatial arrangement of the landscape promotes connectivity or creates barriers to gene flow, directly affecting speciation processes. In this study, we carried out a landscape genomics analysis using NextRAD data from a montane forest specialist bird complex, the Mesoamerican Chestnut-capped/Green-striped Brushfinch of the genus Arremon. Specifically, we examined population genomic structure using different assignment methods and genomic differentiation and diversity, and we tested alternative genetic isolation hypotheses at the individual level (e.g., isolation by barrier, IBB; isolation by environment, IBE; isolation by resistance, IBR). We found well-delimited genomic structuring (K = 5) across Mesoamerican montane forests in the studied group. Individual-level genetic distances among major montane ranges were mainly explained by IBR hypotheses in this sedentary Neotropical taxon. Our results uncover genetic distances/differentiation and patterns of gene flow in allopatric species that support the role of tropical mountains as spatial landscape drivers of biodiversity. IBR clearly supports a pattern of conserved niche-tracking of suitable habitat conditions and topographic complexity throughout glacial-interglacial dynamics.

Genomic scale data shows that Parastacus nicoleti encompasses more than one species of burrowing continental crayfishes and that lineage divergence occurred with and without gene flow.

Delimiting species is a challenge, especially in scenarios of diversification with gene flow and when species are now allopatric where reproductive isolation cannot be directly tested. Continental burrowing crayfishes of the genus Parastacus present a disjoint distribution in southern South America. One of the species is P. nicoleti, which lives in underground waters in swampy and wooded areas of southern Chile. A previous assessment based on mitochondrial DNA sequences suggest that the taxon may represent a species complex. Here, using thousands of nuclear genomic single-nucleotide polymorphisms obtained via RADSeq from 81 specimens collected at 27 localities throughout the distributional range of the species, we apply an integrative species delimitation approach to test species boundaries and to investigate some aspects of the speciation process. Our analyses corroborate previous results; a scenario that we favor suggests that the P. nicoleti encompasses seven distinct species. Additionally, demographic analyses show that the distinct species have followed distinct trajectories in size change during the last 17.5 million years and that speciation in this group occurred both in strict isolation as well as in the presence of gene flow.

Morphological and genetic diversification of Russula floriformis, sp. nov., along the Isthmus of Panama.

Species of Russula are ubiquitous members of ectomycorrhizal fungal communities in tropical ecosystems. However, an important part of the total tropical diversity of this genus and its biogeographic patterns is unknown due to the lack of studies on Russula in tropical ecosystems. We combined molecular, morphological, ecological, and biogeographic data to elaborate concepts for two new subspecies of R. floriformis (subsection Substriatinae). Russula floriformis subsp. floriformis and R. floriformis subsp. symphoniae are described as new from montane forest dominated by Quercus and/or Oreomunnea (Fagales) from Colombia and Panama, respectively. Phylogenies were constructed using nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S), and partial regions of the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-alpha (tef1). Similar environmental conditions, similar morphology, and an ITS sequence similarity higher than 99% with only three different positions indicate that these two subspecies are closely related. Detailed observations of microscopic structures and analyses of further DNA loci, however, revealed morphological and molecular characteristics that allow distinguishing the two subspecies of R. floriformis. Spatial distribution and phylogenetic proximity of the two Russula subspecies and their ectomycorrhizal hosts, i.e., species of Quercus, suggest that their diversification is a result of comigration, adaptation, and geographic isolation along the Isthmus of Panama during the Pliocene and Pleistocene.

Behavioural response to songs between genetically diverged allopatric populations of Darwin's small tree finch in the Galápagos.

Empirical data that identify contemporary mechanisms of divergence shed light on how species could multiply. In this study, we measured population genetic structure, song syllable diversity and response to simulated intruder song in Darwin's small tree finch (Camarhynchus parvulus) on Santa Cruz and Floreana Islands, Galápagos archipelago. Our aim was to test whether the magnitude of contemporary behavioural response in resident birds was consistent with patterns of genetic or cultural differences between populations. We analysed genetic structure and the occurrence of song syllable types, and experimentally measured the response of resident birds to intruder bird song from different geographical origin (i.e., island) or syllable type. We discovered a weak signal of population genetic structure between Santa Cruz and Floreana Islands. Although some song syllables occurred on both islands, others were unique to each island; Santa Cruz Island males used more unique syllables than Floreana Island males. Both Santa Cruz and Floreana resident males discriminated their response towards a simulated intruder song based on the geographical origin of the intruder song, but not on the syllable type sung by the intruder. We conclude that the populations are diverging in genetic and cultural traits and identified a signal of contemporary behavioural response that could maintain divergence upon secondary contact.

Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis.

Knowledge of how animal species use food resources available in the environment can increase our understanding of many ecological processes. However, obtaining this information using traditional methods is difficult for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an environmental DNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the genus Ctenomys distributed in southern and midwestern Brazil. The metabarcoding approach revealed that these species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The family Poaceae was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and molecular operational taxonomic units consumed, mainly among the southern species. Interspecific differences in diet composition were influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.

A second species of Araucariocladus Silveira amp; Mermudes, with notes on the variation in antennomere numbers in this genus (Coleoptera: Lampyridae).

Here, we describe Araucariocladus amfractus sp. nov., and compare it to the previously monotypic type-species, A. hiems. The new species can be distinguished from A. hiems by the following combination: colour pattern overall dark-brown; pedicel three times shorter than antennomere III and slightly wider than long; distance between antennal sockets as wide as 3/5 clypeal width; labial palpomere III with sides divergent towards apex, apical margin longer than dorsal and shorter than ventral margin; pronotum 1.5x wider than long, anterior margin somewhat sinuose, with a shallow angle anteriad, posterior margin almost straight. A. amfractus sp. nov. is, prima facie, endemic to the Itatiaia Massif, part of the Mantiqueira Mountain Range, Southeastern Brazil. We provide illustrations of the diagnostic features, and an occurrence map for the Araucariocladus species. Finally, we report a previously unrecognized intra-specific variation in the antennomere numbers of A. hiems, a feature also present in Araucariocladus amfractus sp. nov., and adjust the generic diagnosis to include species with 17 or 18 antennomeres. [Zoobank LSID: urn:lsid:zoobank.org:act:C335B064-FBD4-4256-983D-B17DF06BAA0D].

A new nurse frog of Allobates masniger-nidicola complex (Anura, Aromobatidae) from the east bank of Tapajós River, eastern Amazonia.

The small nurse frogs of the genus Allobates (Anura, Aromobatidae) represent one of the most challenging taxonomic issues of the Neotropics. During several amphibian surveys in the Middle Tapajós River region, state of Pará, Brazil, we collected phenotypic, ecological, and molecular data on species of this genus, leading to the identification of a new species included in the Allobates masniger-nidicola complex. The new species is characterized by a large body size (snout-vent length 19.2-21.7 mm in males and 19.3-22.0 mm in females), finger III not swollen in adult males; cryptic external coloration, with dorsum uniformly ochre; a dark brown lateral stripe and a pale cream ventrolateral stripe; limbs ranging from ochre to orange; throat and chest violaceous in males and yellowish in females. The advertisement call is usually arranged in bouts of four closely spaced notes, which we term 4-pulsed units of repetition (UR), 0.317 s long on average, followed by silent intervals, and an average dominant frequency of 4.163 kHz. The new species also has exotrophic tadpoles with a unique fin morphology, which begins after the body-tail insertion and is deeper posteriorly to half of the caudal length. Sequencing of the 16S and COI regions of the mitochondrial DNA show a genetic p-distance of approximately 6-10% compared to closely related congeners. We discuss the biogeography of the new species based on phylogenetic relationships of the species within the Allobates masniger-nidicola complex and the allopatric geographic distribution in relation to sister taxa. Functional characteristics and geographic restrictions make this species particularly sensitive to the increasing human impact in eastern Amazonia.

Geography of speciation affects rate of trait divergence in haemulid fishes.

Speciation and the interactions between recently diverged species are thought to be major causes of ecological and morphological divergence in evolutionary radiations. Here, we explore the extent to which geographical overlap and time since speciation may promote divergence in marine species, which represent a small fraction of currently published studies about the patterns and processes of speciation. A time-calibrated molecular phylogeny of New World haemulid fishes, a major radiation of reef and shore fishes in the tropical West Atlantic and East Pacific, reveals 21 sister species pairs, of which eight are fully sympatric and 13 are allopatric. Sister species comparisons show a non-significant relation between most of the phenotypic traits and time since divergence in allopatric taxa. Additionally, we find no difference between sympatric and allopatric pairs in the rate of divergence in colour pattern, overall body shape, or functional morphological traits associated with locomotion or feeding. However, sympatric pairs show a significant decrease in the rate of divergence in all of these traits with increasing time since their divergence, suggesting an elevated rate of divergence at the time of speciation, the effect of which attenuates as divergence time increases. Our results are consistent with an important role for geographical overlap driving phenotypic divergence early in the speciation process, but the lack of difference in rates between sympatric and allopatric pairs indicates that the interactions between closely related species are not dominant drivers of this divergence.

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes.

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.

Reproductive ecology and isolation of Psittacanthus calyculatus and P. auriculatus mistletoes (Loranthaceae).

BACKGROUND: Relationships between floral biology and pollinator behavior are important to understanding species diversity of hemiparasitic Psittacanthus mistletoes (c. 120 species). We aimed to investigate trait divergence linked to pollinator attraction and reproductive isolation (RI) in two hummingbird-pollinated and bird-dispersed Psittacanthus species with range overlap. METHODS: We investigated the phylogenetic relationships, floral biology, pollinator assemblages, seed dispersers and host usage, and the breeding system and female reproductive success of two sympatric populations of P. calyculatus and P. auriculatus, and one allopatric population of P. calyculatus. Flowers in sympatry were also reciprocally pollinated to assess a post-mating component of RI. RESULTS: Hummingbird assemblages differed between calyculatus populations, while allopatric plants of calyculatus opened more but smaller flowers with longer lifespans and produced less nectar than those in sympatry. Bayesian-based phylogenetic analysis indicated monophyly for calyculatus populations (i.e. both populations belong to the same species). In sympatry, calyculatus plants opened more and larger flowers with longer lifespans and produced same nectar volume than those of auriculatus; populations shared pollinators but seed dispersers and host usage differed between species. Nectar standing crops differed between sympatric populations, with lower visitation in calyculatus. Hand pollination experiments indicated a predominant outcrossing breeding system, with fruit set after interspecific pollination two times higher from calyculatus to auriculatus than in the opposite direction. CONCLUSIONS: Given the low genetic differentiation between calyculatus populations, observed trait divergence could have resulted from changes regarding the local communities of pollinators and, therefore, expected divergence for peripheral, allopatric populations. Using RI estimates, there were fewer heterospecific matings than expected by chance in P. calyculatus (RI4A = 0.629) as compared to P. auriculatus (RI4A = 0.20). When considering other factors of ecological isolation that affect co-occurrence, the RI4C values indicate that isolation by hummingbird pollinators was less effective (0.20) than isolation by host tree species and seed dispersers (0.80 and 0.60, respectively), suggesting that host usage is the most important ecological isolation factor between the two species. Accordingly, the absolute and relative cumulative strength values indicated that the host tree species' barrier is currently contributing the most to maintaining these species in sympatry.

Comparative phylogeography of co-distributed Phrygilus species (Aves, Thraupidae) from the Central Andes.

The Neotropical ecoregion has been an important place of avian diversification where dispersal and allopatric events coupled with periods of active orogeny and climate change (Late Pliocene-Pleistocene) have shaped the biogeography of the region. In the Neotropics, avian population structure has been sculpted not only by geographical barriers, but also by non-allopatric factors such as natural selection and local adaptation. We analyzed the genetic variation of six co-distributed Phrygilus species from the Central Andes, based on mitochondrial and nuclear markers in conjunction with morphological differentiation. We examined if Phrygilus species share patterns of population structure and historical demography, and reviewed the intraspecific taxonomy in part of their geographic range. Our results showed different phylogeographic patterns between species, even among those belonging to the same phylogenetic clade. P. alaudinus, P. atriceps, and P. unicolor showed genetic differentiation mediated by allopatric mechanisms in response to specific geographic barriers; P. gayi showed sympatric lineages in northern Chile, while P. plebejus and P. fruticeti showed a single genetic group. We found no relationship between geographic range size and genetic structure. Additionally, a signature of expansion was found in three species related to the expansion of paleolakes in the Altiplano region and the drying phase of the Atacama Desert. Morphological analysis showed congruence with molecular data and intraspecific taxonomy in most species. While we detected genetic and phenotypic patterns that could be related to natural selection and local adaptation, our results indicate that allopatric events acted as a major factor in the population differentiation of Phrygilus species.

Evidence for nonallopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert.

The genetic structure of populations of closely related, sympatric species may hold the signature of the geographical mode of the speciation process. In fully allopatric speciation, it is expected that genetic differentiation between species is homogeneously distributed across the genome. In nonallopatric speciation, the genomes may remain undifferentiated to a large extent. In this article, we analyzed the genetic structure of five sympatric species from the plant genus Heliotropium in the Atacama Desert. We used amplified fragment length polymorphisms (AFLPs) to characterize the genetic structure of these species and evaluate their genetic differentiation as well as the number of loci subject to positive selection using divergence outlier analysis (DOA). The five species form distinguishable groups in the genetic space, with zones of overlap, indicating that they are possibly not completely isolated. Among-species differentiation accounts for 35% of the total genetic differentiation (F ST = 0.35), and F ST between species pairs is positively correlated with phylogenetic distance. DOA suggests that few loci are subject to positive selection, which is in line with a scenario of nonallopatric speciation. These results support the idea that sympatric species of Heliotropium sect. Cochranea are under an ongoing speciation process, characterized by a fluctuation of population ranges in response to pulses of arid and humid periods during Quaternary times.

Distribution patterns and trophic characteristics of salmonids and native species inhabiting high altitude rivers of Pampa de Achala region, Argentina

The Pampa de Achala in central Argentina is an area with low fish species richness where salmonids were first introduced at the beginning of the twentieth century. A total of 19 rivers of different order were sampled during the low water period by using portable electrofishing equipment. We covered different identified macrohabitats (pools, riffles, glides and cascades) in reaches of 300-500 m length. The native species Trichomycterus corduvensis and two exotic salmonids such as Salvelinus fontinalis and Oncorhynchus mykiss represented the most common species, showing allopatric and sympatric distribution in some streams. Stomach contents and diet overlapping were also analyzed. Cluster results showed a first main group comprised those streams with high diet similitude between T. corduvensis and O. mykiss whereas a second main group consisted of streams with high diet similitude between O. mykiss and S. fontinalis. Mean niche width was similar among all these species but T. corduvensis showed that widest range whereas S. fontinalis exhibited the narrowest trophic niche. We were able to document a direct predation on T. corduvensis by O. mykiss in two stream although distribution overlapping among native and exotic species were low. In turn diet overlapping among species were negligible. Trophic niche amplitude of S. fontinalis was inversely related to stream order, providing clues that geomorphology and hydrology may exert also influence of trophic characteristics and can be used for predicting the potential for food competition with native species. Analysis by Tokeshi plot revealed that T. corduvensis ranged from specialist to generalist whereas both salmonids showed generalist feeding habits with a heterogeneous and homogeneous diet.(AU)

El área de Pampa de Achala, en el centro de Argentina, posee una baja riqueza específica y donde los salmónidos fueron introducidos al comienzo del siglo XX. Se muestrearon 19 ríos de diferente orden durante el período de aguas bajas utilizando un equipo de pesca eléctrica portátil. Se cubrieron diferentes macrohábitats (pozones, correderas, tablas y cascadas) en tramos de 300 a 500 m de longitud. Las especie nativa Trichomycterus corduvensis y dos salmódios exóticos, Salvelinus fontinalis y Oncorhynchus mykiss, representaron las especies más comunes mostrando distribuiciones alopátricas y simpátricas en algunos de estos ríos. Se analizaron los contenidos estomacales y la superposición de sus dietas. El análisis por agrupamiento puso en evidencia un primer gran grupo compuesto por aquellos ríos con alta similitud de dieta entre T. corduvensis y O. mykiss, ancho medio de nicho fue similar entre estas especies pero T. corduvensis exhibió el rango de mayor amplitud y S. fontinalis que la superposición de distribución entre especies nativas y exóticas fue escasa. Por su parte, la superposición de dietas entre estas especies fue muy baja. La amplitud de nicho trófico de S. fontinalis estuvo inversamente correlacionada con el orden del río, proporcionando indicios que la geomorfología y hidrología podrían influir sobre las características tróficas y podrían ser utilizadas para predecir la competencia potencial con las especies nativas . El análisis mediante gráficos de Tokeshi reveló que T. corduvensis se comportó como especialista a generalista mientras ambos salmónidos mostraron hábitos generalistas con dietas homogéneas y heterogéneas.(AU)

Distribution patterns and trophic characteristics of salmonids and native species inhabiting high altitude rivers of Pampa de Achala region, Argentina

The Pampa de Achala in central Argentina is an area with low fish species richness where salmonids were first introduced at the beginning of the twentieth century. A total of 19 rivers of different order were sampled during the low water period by using portable electrofishing equipment. We covered different identified macrohabitats (pools, riffles, glides and cascades) in reaches of 300-500 m length. The native species Trichomycterus corduvensis and two exotic salmonids such as Salvelinus fontinalis and Oncorhynchus mykiss represented the most common species, showing allopatric and sympatric distribution in some streams. Stomach contents and diet overlapping were also analyzed. Cluster results showed a first main group comprised those streams with high diet similitude between T. corduvensis and O. mykiss whereas a second main group consisted of streams with high diet similitude between O. mykiss and S. fontinalis. Mean niche width was similar among all these species but T. corduvensis showed that widest range whereas S. fontinalis exhibited the narrowest trophic niche. We were able to document a direct predation on T. corduvensis by O. mykiss in two stream although distribution overlapping among native and exotic species were low. In turn diet overlapping among species were negligible. Trophic niche amplitude of S. fontinalis was inversely related to stream order, providing clues that geomorphology and hydrology may exert also influence of trophic characteristics and can be used for predicting the potential for food competition with native species. Analysis by Tokeshi plot revealed that T. corduvensis ranged from specialist to generalist whereas both salmonids showed generalist feeding habits with a heterogeneous and homogeneous diet.

El área de Pampa de Achala, en el centro de Argentina, posee una baja riqueza específica y donde los salmónidos fueron introducidos al comienzo del siglo XX. Se muestrearon 19 ríos de diferente orden durante el período de aguas bajas utilizando un equipo de pesca eléctrica portátil. Se cubrieron diferentes macrohábitats (pozones, correderas, tablas y cascadas) en tramos de 300 a 500 m de longitud. Las especie nativa Trichomycterus corduvensis y dos salmódios exóticos, Salvelinus fontinalis y Oncorhynchus mykiss, representaron las especies más comunes mostrando distribuiciones alopátricas y simpátricas en algunos de estos ríos. Se analizaron los contenidos estomacales y la superposición de sus dietas. El análisis por agrupamiento puso en evidencia un primer gran grupo compuesto por aquellos ríos con alta similitud de dieta entre T. corduvensis y O. mykiss, ancho medio de nicho fue similar entre estas especies pero T. corduvensis exhibió el rango de mayor amplitud y S. fontinalis que la superposición de distribución entre especies nativas y exóticas fue escasa. Por su parte, la superposición de dietas entre estas especies fue muy baja. La amplitud de nicho trófico de S. fontinalis estuvo inversamente correlacionada con el orden del río, proporcionando indicios que la geomorfología y hidrología podrían influir sobre las características tróficas y podrían ser utilizadas para predecir la competencia potencial con las especies nativas . El análisis mediante gráficos de Tokeshi reveló que T. corduvensis se comportó como especialista a generalista mientras ambos salmónidos mostraron hábitos generalistas con dietas homogéneas y heterogéneas.