Speciation Scenarios Research Articles

Integrative taxonomy reveals a new species of deep-sea squat lobster (Galatheoidea, Munidopsidae) from cold seeps in the Gulf of Mexico

The western Atlantic Ocean harbors a diverse fauna of squat lobsters, particularly in the family Munidopsidae. This study introduces Munidopsis sednasp. nov., a species only found in the Gulf of Mexico and the first species reported to be endemic to cold seeps in the western Atlantic. Our investigation incorporates morphological analyses including micro-CT scanning evidence, multilocus molecular phylogeny, and mtDNA phylogeography, as well as ecological data derived from in situ observations and geographic distribution patterns to substantiate the recognition of the new species. Shallow molecular divergences and multiple morphological differences differentiate the new species from its closest relative, M. longimanus (A. Milne-Edwards, 1880). Additionally, we explore the potential scenario for ecological speciation within this newly identified taxon and discuss its significance in the context of conservation efforts in the Gulf of Mexico.

Geographical and ecological allopatry effects on niche change in two sister species pairs of hummingbirds in western North America

Here, we explored how variations in the allopatric speciation scenario, specifically ecological vs. vicariant allopatry, relate to climatic niche change in sister species. We selected two sister species pairs of North American hummingbirds (Calypte anna, C. costae, Basilinna leucotis, B. xantusii) that diverged 2.5 and 3.6 million years ago, under ecological (arid climate tendency during Pliocene) and vicariant (Baja California peninsula separation) allopatric processes, respectively. We constructed the climatic niche of each species using occurrence records and estimated the distance, similarity, and unique fraction of climatic niche between sister species. Calypte species showed moderate niche divergence (Euclidean distance between centroids = 1.94, Sørensen index of similarity = 0.080, unique fraction of hypervolume in C. costae = 0.57, and C. anna = 0.95). However, contrary to expectations, Basilinna species, which diverged under a vicariant scenario, displayed clear niche divergence (Euclidean distance between centroids = 3.78, Sørensen index of similarity = 0.0001, and unique fraction of hypervolume in B. xantusii = 0.98, and B. leucotis = 0.99). We explained dissimilarity in climatic niches between Basilinna species by the ecological divergence between habitats of disjunct populations, which would have also been associated with increased aridity during the Pliocene.

Population dynamics and games of variable size

This work introduces the concept of Variable Size Game Theory (VSGT), in which the number of players in a game is a strategic decision made by the players themselves. We start by discussing the main examples in game theory: dominance, coexistence, and coordination. We show that the same set of pay-offs can result in coordination-like or coexistence-like games depending on the strategic decision of each player type. We also solve an inverse problem to find a d-player game that reproduces the same fixation pattern of the VSGT. In the sequel, we consider a game involving prosocial and antisocial players, i.e., individuals who tend to play with large groups and small groups, respectively. In this game, a certain task should be performed, that will benefit one of the participants at the expense of the other players. We show that individuals able to gather large groups to perform the task may prevail, even if this task is costly, providing a possible scenario for the evolution of eusociality. The next example shows that different strategies regarding game size may lead to spontaneous separation of different types, a possible scenario for speciation without physical separation (sympatric speciation). In the last example, we generalize to three types of populations from the previous analysis and study compartmental epidemic models: in particular, we recast the SIRS model into the VSGT framework: Susceptibles play 2-player games, while Infectious and Removed play a 1-player game. The SIRS epidemic model is then obtained as the replicator equation of the VSGT. We finish with possible applications of VSGT to be addressed in the future.

Biogeography, speciation and niche evolution of doraditos (Aves: Pseudocolopteryx)

AbstractEcological and geographical factors shape the current distribution of species. Analysing their interplay in a phylogenetic framework is key to understand the historical processes that have shaped the evolution of a group. Here, we modelled the ecological niches and geographic distributions of the five species of doraditos (Pseudocolopteryx spp.) to study their biogeographic histories, niche evolution and speciation process in a phylogenetic framework. Our potential distribution models uncovered novel range‐wide distributional patterns and seasonal movements in the doraditos, where four species are migratory with distinct breeding and non‐breeding distributions, and one (P. sclateri) exhibits a complex spatiotemporal distribution indicating nomadism. Ecological niche pairwise comparisons showed that none of the doraditos have equivalent niches and that niche differences are due to species‐specific habitat preferences. Phylogenetically weighted geographical and ecological analyses showed patterns of allopatric speciation and niche lability in the evolution of doraditos. The divergence of P. sclateri seems tied to its tropical‐to‐temperate wetland specialization. The montane P. acutipennis expanded to human‐modified lowlands following speciation, highlighting the need to control for post‐speciational changes in ecological niche comparisons as done here. In turn, P. dinelliana, P. citreola and P. flaviventris showed essentially allopatric breeding distributions, as a product of environmentally mediated divergence during their speciation processes. The distribution and migration data of the recently diverged cryptic sister species P. citreola and P. flaviventris are consistent with two possible speciation scenarios: peripatric speciation and migration dosing speciation.

Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae).

Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid-polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.

Ecological speciation in sympatric palms: 5. Evidence for pleiotropic speciation genes using gene knockout and high-throughput phenotyping

Abstract Theoretical models predict that sympatric, ecological speciation may be facilitated more readily when so-called ‘magic traits’ are present, linking traits under divergent selection with assortative mating. Such traits might be encoded by pleiotropic genes, that is, genes that affect multiple, apparently unrelated, phenotypes. However, few convincing examples of sympatric speciation exist, and empirical evidence for the role of magic traits in driving such speciation is rare. One of the strongest cases of sympatric speciation is the Howea palms of Lord Howe Island, Australia, comprising the sister species Howea belmoreana and Howea forsteriana, which have diverged due to soil substrate preferences and flowering time displacement. Here we investigate the role that pleiotropy may have played in the speciation process by carrying out high-throughput phenotyping experiments using 1830 Arabidopsis thaliana plants with knockouts of candidate Howea ‘speciation genes’. We identify several genes that show signatures of adaptive divergence between the Howea species and demonstrate pleiotropic roles in soil stress tolerance and flowering time, consistent with the Howea speciation scenario—notably, Howea orthologues of the A. thaliana loci At2-MMP, DCL1, RCD1, SAL1, and SIZ1. Empirical evidence is provided, therefore, for a range of pleiotropic genes with the potential to have driven sympatric speciation by generating magic traits which link divergent selection to non-random mating.

On the specific status of eastern Mediterranean Dendrophyllia corals (Cnidaria, Anthozoa): Genetic characterization and speciation scenarios

AbstractThe deep‐sea corals Dendrophyllia ramea and Dendrophyllia cornigera occur in Mediterranean and Atlantic waters. Both species are found in different environmental conditions, and they can colonize hard and soft substrates. These species then display an important ecological plasticity along with morphological plasticity. Nevertheless, there is a large knowledge gap on the genetic characteristics of the two species, including on the relationships between them and the possibility of cryptic species along their range. The recent discovery of Dendrophyllia populations off Cyprus in the eastern Mediterranean Sea raised new questions in this context. These corals were related to D. ramea but had some morphological differences with other known populations of this species. Here, we study the specific status of Dendrophyllia corals from Cyprus on the basis of morphology and genetics. The genetic data are interpreted by comparison with the same analysis performed on two Caryophyllia species. Both morphological and genetic data confirm that corals found off Cyprus belong to the D. ramea species. We further tested the speciation scenario using transcriptome data: the results indicate an absence of current gene flow between D. ramea and D. cornigera and that the divergence occurred more than 3 million years ago. We discuss the possible historical and ecological factors which may have shaped speciation in these species.

Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes

The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme’s sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.

Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains

Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome.Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes.Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species.In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios.Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses.We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.

How Important Is Budding Speciation for Comparative Studies?

The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with 3 or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here, we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here, we show that many PCMs assume that divergence happens as a symmetric split, even if these methods do not explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.

More hidden diversity in a cryptic species complex: a new subspecies of Leptideasinapis (Lepidoptera, Pieridae) from Northern Iran.

A new subspecies of Leptideasinapis from Northern Iran, discovered by means of DNA barcoding, is described as Leptideasinapistabarestanassp. nov. The new subspecies is allopatric with respect to other populations of L.sinapis and is genetically distinct, appearing as a well-supported sister clade to all other populations in COI-based phylogenetic reconstructions. Details on karyotype, genitalia, ecology and behaviour for the new subspecies are given and a biogeographical speciation scenario is proposed.

Population genomic analyses support sympatric origins of parapatric morphs in a salamander.

In numerous clades, divergent sister species have largely non-overlapping geographic ranges. This pattern presumably arises because species diverged in allopatry or parapatry, prior to a subsequent contact. Here, we provide population-genomic evidence for the opposite scenario: previously sympatric ecotypes that have spatially separated into divergent monomorphic populations over large geographic scales (reverse sympatric scenario). We analyzed a North American salamander (Plethodon cinereus) with two color morphs that are broadly sympatric: striped (redback) and unstriped (leadback). Sympatric morphs can show considerable divergence in other traits, and many Plethodon species are fixed for a single morph. Long Island (New York) is unusual in having many pure redback and leadback populations that are spatially separated, with pure redback populations in the west and pure leadbacks in the east. Previous work showed that these pure-morph populations were genetically, morphologically, and ecologically divergent. Here, we performed a coalescent-based analysis of new data from 88,696 single-nucleotide polymorphisms to address the origins of these populations. This analysis strongly supports the monophyly of Long Island populations and their subsequent divergence into pure redback and pure leadback populations. Taken together, these results suggest that the formerly sympatric mainland morphs separated into parapatric populations on Long Island, reversing the conventional speciation scenario.

Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact.

Closely related taxa frequently exist in sympatry before the evolution of robust reproductive barriers, which can lead to substantial gene flow. Post-divergence gene flow can promote several disparate trajectories of divergence ranging from the erosion of distinctiveness and eventual collapse of the taxa to the strengthening of reproductive isolation. Among many relevant factors, understanding the demographic history of divergence (e.g. divergence time and extent of historical gene flow) can be particularly informative when examining contemporary gene flow between closely related taxa because this history can influence gene flow's prevalence and consequences. Here, we used genotyping-by-sequencing data to investigate speciation and contemporary hybridization in two closely related and sympatrically distributed Lake Tanganyikan cichlid species in the genus Petrochromis. Demographic modelling supported a speciation scenario involving divergence in isolation followed by secondary contact with bidirectional gene flow. Further investigation of this recent gene flow found evidence of ongoing hybridization between the species that varied in extent between different co-occurring populations. Relationships between abundance and the degree of admixture across populations suggest that the availability of conspecific mates may influence patterns of hybridization. These results, together with the observation that sets of recently diverged cichlid taxa are generally geographically separated in the lake, suggest that ongoing speciation in Lake Tanganyikan cichlids relies on initial spatial isolation. Additionally, the spatial heterogeneity of admixture between the Petrochromis species illustrates the complexities of hybridization when species are in recent secondary contact.

Speciation with gene flow between two Neotropical sympatric species (Pitcairnia spp.: Bromeliaceae).

The study of mechanisms that generate new species is considered fundamental for broad areas of ecology and evolution. Speciation is a continuous process in which reproductive isolation is established, and it is of fundamental importance to understand the origins of the adaptations that contribute to this process. Hybrid zones are considered natural laboratories for the study of speciation and represent ideal systems for such studies. Here, we investigated genomic differentiation between hybridizing Neotropical species Pitcairnia staminea (G. Lodd.) and P. albiflos (Herb.). Using thousands of SNPs genotyped through RAD‐seq, we estimate effective population sizes, interspecific gene flow, as well as time of divergence between these two sister species and identify candidate genomic regions for positive selection that may be related to reproductive isolation. We selected different scenarios of speciation and tested them by using approximate Bayesian computation (ABC); we found evidence of divergence with gradual reduction in gene flow between these species over time, compatible with the hypothesis of speciation with gene flow between these Pitcairnia species. The parameter estimates obtained through ABC suggested that the effective population size of P. albiflos was around three times larger than that of P. staminea. Our divergence date estimates showed that these two species diverged during the Pliocene (4.7 Mya; CI = 1.3–8.5 Mya), which has likely allowed this species to accumulate genome‐wide differences. We also detected a total of 17 of 4165 loci which showed signatures of selection with high genetic differentiation (F ST > 0.85), 12 of these loci were annotated in de novo assembled transcriptomes of both species, and 4 candidate genes were identified to be putatively involved in reproductive isolation. These four candidate genes were previously associated with the function of pollen development, pollen tube germination and orientation, abiotic stress, and flower scent in plants, suggesting an interplay between pre‐ and postpollination barriers in the evolution of reproductive isolation between such species.

DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina

Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. Here, we applied DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analysed 335 COI barcodes in 34morphologically determined species from 39localities along central Andes and arid lands of Argentina. Neighbour-joining and maximum likelihood reconstruction provided clear separation between species. The Barcode Index number and Bayesian Poisson tree processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A.oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) versus a minimum nearest-neighbour distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A.oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.

The evolution of age-specific choosiness and reproductive isolation in a model with overlapping generations.

The strength of mate choice (choosiness) often varies with age, but theory to understand this variation is scarce. Additionally, theory has investigated the evolution of choosiness in speciation scenarios but has ignored that most organisms have overlapping generations. We investigate whether speciation can result in variation of choosiness with age, and whether such variation can in turn affect speciation. We develop a population-genetic model of the evolution of choosiness in organisms with overlapping generations in the context of secondary contact between two divergent populations. We assume that females choose males that match their phenotype, such that choosiness evolves by sexual selection. We demonstrate that speciation can result in the evolution of age-specific choosiness when the mating trait is under divergent ecological selection and age is not used as a mating cue. The cause of this result is that allele frequencies differ between choosy females and males. However, we find that the evolution of age-specific choosiness does not affect the overall level of reproductive isolation compared to a case without age-structure, supporting previous speciation theory. Overall, our results connect life history and speciation theory, and the mechanisms that we highlight have implications for the understanding of the role of sex-specific selection in the evolution ofchoosiness.

Species-range-size distributions: Integrating the effects of speciation, transformation, and extinction.

The species‐range size distribution is a product of speciation, transformation of range‐sizes, and extinction. Previous empirical studies showed that it has a left‐skewed lognormal‐like distribution. We developed a new mathematical framework to study species‐range‐size distributions, one in which allopatric speciation, transformation of range size, and the extinction process are explicitly integrated. The approach, which we call the gain‐loss‐allopatric speciation model, allows us to explore the effects of various speciation scenarios. Our model captures key dynamics thought to lead to known range‐size distributions. We also fitted the model to empirical range‐size distributions of birds, mammals, and beetles. Since geographic range dynamics are linked to speciation and extinction, our model provides predictions for the dynamics of species richness. When a species‐range‐size distribution initially evolves away from the range sizes at which the likelihood of speciation is low, it tends to cause diversification slowdown even in the absence of (bio)diversity dependence in speciation rate. Using the mathematical model developed here, we give a potential explanation for how observed range‐size distributions emerge from range‐size dynamics. Although the framework presented is minimalistic, it provides a starting point for examining hypotheses based on more complex mechanisms.

Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species. The mechanism of how speciation in sexually dichromatic species operates in the face of gene flow remains an open question. Two species in the genus Chrysolophus, the Golden Pheasant (C. pictus) and Lady Amherst's Pheasant (C. amherstiae), both of which exhibit significant plumage dichromatism, are currently parapatric in southwestern China with several hybrid recordings in field. In this study, we estimated the pattern of gene flow during the speciation of the two pheasants using the Approximate Bayesian Computation (ABC) method based on data from multiple genes. Using a newly assembled de novo genome of Lady Amherst's Pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by the PSMC (pairwise sequentially Markovian coalescent) method. The results provide clear evidence that the gene flow between the two pheasants was consistent with the predictions of the isolation with migration model during divergence, indicating that there was long-term gene flow after the initial divergence (ca. 2.2 million years ago). The data further support the occurrence of secondary contact between the parapatric populations since around 30 kya with recurrent gene flow to the present, a pattern that may have been induced by the population expansion of the Golden Pheasant in the late Pleistocene. The results of the study support the scenario of speciation between the Golden Pheasant and Lady Amherst's Pheasant with cycles of mixing-isolation-mixing, possibly due to the dynamics of geographical context in the late Pleistocene. The two species provide a good research system as an evolutionary model for testing reinforcement selection in speciation.

Molecular phylogeny and phylogeography of the freshwater-fish genus Pethia (Teleostei: Cyprinidae) in Sri Lanka

BackgroundSri Lanka is a continental island separated from India by the Palk Strait, a shallow-shelf sea, which was emergent during periods of lowered sea level. Its biodiversity is concentrated in its perhumid south-western ‘wet zone’. The island’s freshwater fishes are dominated by the Cyprinidae, characterized by small diversifications of species derived from dispersals from India. These include five diminutive, endemic species of Pethia (P. bandula, P. cumingii, P. melanomaculata, P. nigrofasciata, P. reval), whose evolutionary history remains poorly understood. Here, based on comprehensive geographic sampling, we explore the phylogeny, phylogeography and morphological diversity of the genus in Sri Lanka.ResultsThe phylogenetic analyses, based on mitochondrial and nuclear loci, recover Sri Lankan Pethia as polyphyletic. The reciprocal monophyly of P. bandula and P. nigrofasciata, and P. cumingii and P. reval, is not supported. Pethia nigrofasciata, P. cumingii, and P. reval show strong phylogeographic structure in the wet zone, compared with P. melanomaculata, which ranges across the dry and intermediate zones. Translocated populations of P. nigrofasciata and P. reval in the Central Hills likely originate from multiple sources. Morphological analyses reveal populations of P. nigrofasciata proximal to P. bandula, a narrow-range endemic, to have a mix of characters between the two species. Similarly, populations of P. cumingii in the Kalu basin possess orange fins, a state between the red-finned P. reval from Kelani to Deduru and yellow-finned P. cumingii from Bentara to Gin basins.ConclusionsPolyphyly in Sri Lankan Pethia suggests two or three colonizations from mainland India. Strong phylogeographic structure in P. nigrofasciata, P. cumingii and P. reval, compared with P. melanomaculata, supports a model wherein the topographically complex wet zone harbors greater genetic diversity than the topographically uniform dry-zone. Mixed morphological characters between P. bandula and P. nigrofasciata, and P. cumingii and P. reval, and their unresolved phylogenies, may suggest recent speciation scenarios with incomplete lineage sorting, or hybridization.

Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system.

Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P.aurisetus. Our results highlight the cryptic diversity within the P.aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.