Species identification through deep learning and geometrical morphology in oaks (Quercus spp.): Pros and cons

Plant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf-scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost-efficient method in terms of time-consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.

Philippine herpetology (Amphibia, Reptilia), 20 years on: two decades of progress towards an increasingly collaborative, equitable, and inclusive approach to the study of the archipelago's amphibians and reptiles

A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized the diverse topics studied and highlighted the development and achievements in research up to the year 2000. This study revisits and re-assesses what Philippine herpetology has accomplished, both as a discipline and a community, during the last two decades (2002-2022). A total of 423 herpetological publications was collated, revealing a substantial increase in annual publications, rising from approximately four per year during 2002-2008 to around 28 per year in 2009-2022. Half of the published studies focused on squamate reptiles (lizards 30.5%, snakes 21%) and 28.4% on amphibians, 5.9% on turtles, and 2.6% on crocodiles. The remaining 11.6% of studies focused simultaneously on multiple taxa (i.e., faunal inventories). Diversity and distribution (35.2%) and ecological (26.5%) studies remained popular, while studies on taxonomy (14.9%), phylogenetics and biogeography (11.8%), and conservation (11.6%) all increased. However, geographical gaps persist urging immediate surveys in many understudied regions of the country. Finally, we found a balanced representation between Filipino and foreign first authors (1.0:1.1), yet a substantial gender gap exists between male and female first authors (7.1:1.0). Nonetheless, the steep increase in publications and the diversity of people engaged in Philippine herpetology is a remarkable positive finding compared to the 20 years preceding the last review (1980-2000). Our hope is that the next decades will bring increasingly equitable, internationally collaborative, and broadly inclusive engagement in the study of amphibians and reptiles in the Philippines.

Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)

One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Variation in species richness, composition and herpetological community structure across a tropical habitat gradient of Palawan Island, Philippines

Information on species richness and community structure is invaluable for guiding conservation and management of biodiversity, but is rarely available in the megadiverse biodiversity conservation hotspot of Philippines – particularly for amphibians and reptiles. This study provides the first report and characterisation of amphibians and reptile communities across primary habitat types of the Victoria-Anepahan Mountain Range on Palawan Island along the western edge of the archipelago. A total of 41 amphibian and reptile species were recorded throughout our sampling sites (n = 27 species) or in targeted habitat searches (14 species). A species richness estimator predicted that 35 species may be present in our sampling sites, suggesting that a significant proportion of secretive species may continue to be unrecorded, especially for reptiles. Higher species richness was found in secondary growth than in mixed-use agricultural areas or even pristine forest. The low species richness recorded from pristine forest types may be due to these forests now being restricted to higher elevations where species diversity has been documented to decrease. Our results also show that complex community structures (species assemblages) are to be equally expected in both secondary growth and pristine forests. Together, our results show how species richness and community assemblages may vary across habitats, highlighting that old growth forest does not always support higher species richness, particularly in high elevations.

Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes)

ABSTRACT Catfishes of the family Astroblepidae form a group composed by 82 valid species of the genus Astroblepus inhabiting high-gradient streams and rivers throughout tropical portions of the Andean Cordillera. Little has been advanced in the systematics and biodiversity of astroblepids other than an unpublished thesis, a single regional multilocus study and isolated species descriptions. Here, we examined 208 specimens of Astroblepus that apparently belong to 16 valid species from several piedmont rivers from northern Colombia to southern Peru. Using three single-locus approaches for species delimitation in combination with a species tree analysis estimated from three mitochondrial genes, we identified a total of 25 well-delimited lineages including eight valid and 17 potential undescribed species distributed in two monophyletic groups: the Central Andes Clade, which contains 14 lineages from piedmont rivers of the Peruvian Amazon, and the Northern Andes Clade with 11 lineages from trans- and cis-Andean rivers of Colombia and Ecuador, including the Orinoco, Amazon, and Magdalena-Cauca basins and Pacific coastal drainages. Results of species delimitation methods highlight several taxonomical incongruences in recently described species denoting potential synonymies.

Recent range expansion of an intermediate host for animal schistosome parasites in the Indo-Australian Archipelago: phylogeography of the freshwater gastropod Indoplanorbis exustus in South and Southeast Asia

Background

The planorbid snail Indoplanorbis exustus is the sole intermediate host for the Schistosoma indicum species group, trematode parasites responsible for cattle schistosomiasis and human cercarial dermatitis. This freshwater snail is widely distributed in Southern Asia, ranging from Iran to China eastwards including India and from the southeastern Himalayas to Southeast Asia southwards. The veterinary and medical importance of this snail explains the interest in understanding its geographical distribution patterns and evolutionary history. In this study, we used a large and comprehensive sampling throughout Indo-Malaya, including specimens from South India and Indonesia, areas that have been formerly less studied.

Results

The phylogenetic inference revealed five highly divergent clades (genetic distances among clades: 4.4–13.9%) that are morphologically indistinguishable, supporting the assumption that this presumed nominal species may represent a cryptic species complex. The species group may have originated in the humid subtropical plains of Nepal or in southern adjacent regions in the Early Miocene. The major cladogenetic events leading to the fives clades occurred successively from the Early Miocene to the Early Pleistocene, coinciding with major periods of monsoonal intensification associated with major regional paleogeographic events in the Miocene and repeated climate changes due to the Plio-Pleistocene climatic oscillations. Our coverage of the Indo-Australian Archipelago (IAA) highlights the presence of a single clade there. Contrary to expectations, an AMOVA did not reveal any population genetic structure among islands or along a widely recognised zoogeographical regional barrier, suggesting a recent colonisation independent of natural biogeographical constraints. Neutrality tests and mismatch distributions suggested a sudden demographic and spatial population expansion that could have occurred naturally in the Pleistocene or may possibly result of a modern colonisation triggered by anthropogenic activities.

Conclusions

Even though Indoplanorbis is the main focus of this study, our findings may also have important implications for fully understanding its role in hosting digenetic trematodes. The existence of a cryptic species complex, the historical phylogeographical patterns and the recent range expansion in the IAA provide meaningful insights to the understanding and monitoring of the parasites potential spread. It brings a substantial contribution to veterinary and public health issues.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-2043-6) contains supplementary material, which is available to authorized users.

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands

We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion.

A new blue-tailed Monitor lizard (Reptilia, Squamata, Varanus) of the Varanus indicus group from Mussau Island, Papua New Guinea

We describe a new species of Varanus from Mussau Island, north-east of New Guinea. The new species is a member of the Varanus indicus species group and is distinguished from all other members by both morphological and molecular genetic characters. It is the third species of Varanus reported from the Bismarck Archipelago and the first record of a yellow tongued member of the Varanus indicus species group from a remote oceanic island. The herpetofauna of Mussau Island has not been well studied but the discovery of this new species is in accordance with recent findings indicating that the island may harbor several unknown endemic vertebrates. The distribution of the closely related Varanus finschi is also discussed in the light of recent fieldwork and a review of old records.

Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota)

Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.

Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae)

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

The effects of partitioning on phylogenetic inference

Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.

Taking the discovery approach in integrative taxonomy: decrypting a complex of narrow-endemic Alpine harvestmen (Opiliones: Phalangiidae: Megabunus)

Species delimitation is fundamental for biological studies, yet precise delimitation is not an easy task, and every involved approach has an inherent failure rate. Integrative taxonomy, a method that merges multiple lines of evidence, can profoundly contribute to reliable alpha-taxonomy and shed light on the processes behind speciation. In this study, we explored and validated species limits in a group of closely related Megabunus harvestmen (Eupnoi, Phalangiidae) endemic to the European Alps. Without a priori species hypotheses, we used multiple sources of inference, including mitochondrial and multilocus nuclear DNA, morphometrics and chemistry. The results of these discovery approaches revealed morphological crypsis and multiple new species within two of the five hitherto known species. Based on our analyses, we discussed the most plausible evolutionary scenarios, invoked the most reasonable species hypotheses and validated the new species limits. Building upon the achieved rigour, three new species, Megabunus cryptobergomas Muster and Wachter sp. nov., Megabunus coelodonta Muster and Steiner sp. nov., and Megabunus lentipes Muster and Komposch sp. nov., are formally described. In addition, we provide a dichotomous morphological key to the Megabunus species of the Alps. Our work demonstrates the suitability of integrative, discovery-based approaches in combination with validation approaches to precisely characterize species and enabled us to implement nomenclatural consequences for this genus.

Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate

Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier.

Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia

The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia.

Fossil-calibrated phylogeny and historical biogeography of Southeast Asian water monitors (Varanus salvator Complex)

We utilize robust geographical genetic sampling, a multilocus dataset, a new synthesis of numerous fossil calibration points, a time-calibrated phylogeny, and the Dispersal-Extinction-Cladogenesis model to test the prediction that widespread Southeast Asian water monitor species initially diversified on the Asian mainland and subsequently invaded the island archipelagos of the Philippines, Sundaland, and Wallacea. Our results strongly contradict these expectations and instead infer an initial water monitor radiation of range-restricted but highly divergent evolutionary lineages (now recognized as endemic species) in one archipelago around 3.6 mya, followed by an out-of-the-Philippines reinvasion of the mainland (2.2 mya), resulting in a few, widespread species that now inhabit most the islands of the Sunda Shelf and the Southeast Asian mainland as far north as Myanmar, as well as an out-of-the-Philippines invasion of Sulawesi (2.1 mya). Our analyses both confirm the importance of island archipelagos as drivers of diversification for mainland biodiversity and emphasize the global evolutionary significance and conservation priority of the Philippines for understanding processes of diversification in island archipelagos.

Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

How to fail at species delimitation

Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.