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opencc-zeroJun 2020View details →

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Cryptic species - genetically distinct species that are morphologically difficult to distinguish - present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole usage of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean Bark Anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternate species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

opencc-zeroJun 2020View details →

Data from: Assessing species boundaries in the open sea: an integrative taxonomic approach to the pteropod genus Diacavolinia

To track changes in pelagic biodiversity in response to climate change, it is essential to accurately define species boundaries. Shelled pteropods are a group of holoplanktonic gastropods that have been proposed as bio-indicators because of their vulnerability to ocean acidification. A particularly suitable, yet challenging group for integrative taxonomy is the pteropod genus Diacavolinia, which has a circumglobal distribution and is the most species-rich pteropod genus, with 24 described species. We assessed species boundaries in this genus, with inferences based on geometric morphometric analyses of shell-shape variation, genetic (cytochrome c oxidase subunit I, 28S rDNA sequences) and geographic data. We found support for a total of 13 species worldwide, with observations of 706 museum and 263 freshly collected specimens across a global collection of material, including holo‐ and paratype specimens for 14 species. In the Atlantic Ocean, two species are well supported, in contrast to the eight currently described, and in the Indo‐Pacific we found a maximum of 11 species, partially merging 13 of the described species. Distributions of these revised species are congruent with well-known biogeographic provinces. Combining varied datasets in an integrative framework may be suitable for many diverse taxa and is an important first step to predicting species-specific responses to global change.

opencc-zeroOct 2020View details →

New species boundaries and the diversification history of marsh rat taxa clarify historical connections among ecologically and geographically distinct wetlands of South America

Taxa with broad geographic ranges that occur in different biomes and exhibit plastic morphological traits and/or adaptations to particular habitats make inferences about species boundaries especially challenging. However, technological and conceptual advances in the generation and analysis of genomic data have advanced the description of biodiversity. Here we address the outstanding questions about the delimitation of species in the genus Holochilus, a rodent with morphological specializations to wetland habitats, distributed through almost all the South America continent using genome‐wide SNP and morphometric data. Specifically, we apply a Bayesian model‐based species delimitation that revealed significant re-arrangements of species boundaries based on consideration of both morphometric and genomic data alone, or in combination. With these shifts in species boundaries, our results provide an insightful framework for inferring the group's biogeographic history and considering possible connections between disjoint biomes in South America. Because of the ecological constraints of the marsh rats, and with the proposed taxonomic re-arrangements, the significance of our findings extends beyond systematics and suggests how diversification might be associated with past ecological/environmental changes during the Pleistocene. Overall, this study highlights how genomic data can provide phylogenetic information for resolving relationships among species of Holochilus, but also the importance of integrative approaches to identify evolutionary independent species. For the relatively understudied vast wetlands of South America, a robust species delimitation framework therefore becomes a critical source of data relevant to hypotheses about the history of the biomes themselves.

opencc-zeroFeb 2020View details →

Stable species boundaries despite ten million years of hybridization in tropical eels

Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.

opencc-zeroDec 2018View details →

Data from: Reproductive isolation and the maintenance of species boundaries 1 in two serpentine endemic Jewelflowers

Speciation occurs when reproductive barriers substantially reduce gene flow between lineages. Understanding how specific barriers contribute to reproductive isolation offers insight into the initial forces driving divergence, and the evolutionary and ecological processes responsible for maintaining diversity. Here we quantified multiple pre- and post-pollination isolating barriers in a pair of closely related California Jewelflowers (Streptanthus, Brassicaceae) living in an area of sympatry. S. breweri and S. hesperidis are restricted to similar serpentine habitats, however populations are spatially isolated at fine-scales and rarely co-occur in intermixed stands. Several intrinsic postzygotic barriers were among the strongest we quantified, however postzygotic barriers currently contribute little to overall reproductive isolation due to the cumulative strength of earlier-acting extrinsic barriers, including spatial isolation, and flowering time and pollinator differences. Data from multiple years suggest that pre-pollination barriers may have different strengths depending on annual environmental conditions. Similarly, crossing data suggest that the strength of intrinsic isolation may vary between different population pairs. Estimates of total reproductive isolation in S. breweri - S. hesperidis are robust to uncertainty and variability in individual barrier strength estimates, demonstrating how multiple barriers can act redundantly to prevent gene flow between close relatives living in sympatry.

opencc-zeroDec 2021View details →

UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction

The genus Cryptopone Emery contains 25 species of litter and soil ants, 5 of which occur in the Americas. Cryptoponegilva occurs in the southeastern U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon biogeographic disjunction observed most often in plants. We used phylogenomic data from ultraconserved elements (UCEs), as well as mitogenomes and legacy markers, to investigate phylogenetic relationships, species boundaries, and divergence dates among New World Cryptopone. Species delimitation was conducted using a standard approach and then tested using model-based molecular methods (SNAPP, BPP, SODA, and bPTP). We found that Cryptopone as currently constituted is polyphyletic, and that all the South American species belong to Wadeura Weber, a separate genus unrelated to Cryptopone. A single clade of true Cryptopone occurs in the Americas, restricted to North and Central America. This clade is composed of four species that originated ~4.2 million years ago. One species from the mountains of Guatemala is sister to the other three, favoring a vicariance hypothesis of diversification. The taxonomy of the New World Cryptoponeand Wadeura are revised. Taxonomic changes are: Wadeura Weber is resurrected, with new combinations W. guianensisWeber, W. holmgreni (Wheeler), and W. pauli (Fernandes & Delabie); C. guatemalensis (Forel) (rev. stat.) is raised to species, and includes C. obsoleta (Menozzi) (syn. nov.). The following new species are described: Cryptopone gilvagrande, C. gilvatumida, and Wadeura holmgrenita. Cryptopone hartwigi is transferred to Fisheropone (n. comb.). Cryptopone mirabilis (Mackay & Mackay 2010) is a junior synonym of Centromyrmex brachycola (Roger) (syn. nov.).

opencc-zeroFeb 2022View details →

Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding i) species-level diversity, ii) hybridization and admixture, and iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation. --

opencc-zeroOct 2022View details →

Host preference of a tree-killing bark beetle across a geographic boundary separating host species

The life cycles of bark beetles are intimately linked to their host species. Therefore, bark beetle species are expected to show traits that vary among different host species and across geographic ranges. The taxonomic proximity of host tree species can also influence host selection. Abies species native to Japan are genetically classified into three phylogenetic groups. Their natural distributions are separated by a distinct biogeographic boundary in Japan (i.e. the Tsugaru Strait, also referred to as Blakiston's Line). Especially, A. sachalinensis is the only species native to Hokkaido, north of the Tsugaru Strait. I, therefore, investigated the host preference of Polygraphus proximus Blandford within four allopatrically distributed Abies species across the north and south of the Tsugaru Strait through field surveys and field choice experiments. Field observations and field host-choice bioassays showed that A. sachalinensis was less severely attacked by P. proximus than was A. veitchii on both sides of the Tsugaru Strait. The beetles also preferred to attack A. firma (which belongs to a genetically distinct group (i.e., the section Momi) from that of A. veitchii and A. sachalinensis (i.e., the section Balsamea)), over A. sachalinensis in both Hokkaido and Honshu. Although A.homolepis also belongs to the section Momi, A. firma and A. veitchii had more attacks than A. homolepis. The results provide evidence that P. proximus does not show specialization across the different parts of their geographic range where the host species are different, and there is no positive correlation between taxonomic proximity and host preference for P. proximus.

opencc-zeroJul 2024View details →

Data from: Phylogenomic loci define the generic boundaries of Gochnatieae and improve resolution at the species level in Moquiniastrum (Compositae)

Understanding the evolution of the tribe Gochnatieae (Compositae) has been the subject of considerable effort in the past decade. This is due to the key position of this tribe in the phylogeny of the sunflower family and the corresponding implications for biogeographic and morphological evolution of Compositae. Previous studies have confirmed the monophyly of this tribe as well as most of the genera that belong to it. However, phylogenetic resolution of Gochnatieae at both the genus- and species-level has remained poor. A subset of new phylogenomic loci used in this study has proven effective and has improved phylogenetic resolution in this group. The results of this work demonstrate Gochnatieae is a well-supported clade comprised of nine genera (Anastraphia, Cnicothamnus, Cyclolepis, Gochnatia, Moquiniastrum, Nahuatlea, Pentaphorus, Richterago, Tehuasca). One recently described genus, Vickia, was not included in this study; but its placement in Gochnatieae as a tenth genus in the tribe is well-justified. The monospecific Cyclolepis, which had been circumscribed within the tribe since its inception but was subsequently removed and designated as incertae sedis since 2014, is also shown to belong to Gochnatieae. We confirmed the monophyletic Moquiniastrum with two well-supported subclades. Ancestral area reconstruction analyses show that Gochnatieae originated in Eastern South America about 53 my. Apparently, except for Cyclolepis and Richterago, the ancestors of the other genera of Gochnatieae originated about 44 my from an area that now corresponds to the central Andes. The presence of the genera in the Chaco phytogeographic province, central Chile, and Mexico-United States-Caribbean is a result of dispersal from the central Andes. The ancestral distribution of Moquiniastrum corresponds to a large area comprising Eastern South America and the current central Andes, about 32 my. Ancestral character state reconstruction that included four characters indicates several states associated with complex plant reproductive biology such as gynodioecy, gynomonoecy, and polygamodioecy are derived in Gochnatieae as are heterogamous capitula (in Moquiniastrum and Richterago), dimorphic and subdimorphic corollas (in Cnicothamnus, Moquiniastrum, and Richterago), and the presence of marginal female corollas (in Moquiniastrum and Richterago). Within Moquiniastrum, two subclades (Densicephalum and Polymorphum) exhibit divergent patterns of trait evolution associated with these reproductive characters which suggests this genus can serve as a model to understand the sexual system evolution in plants.

Fig. 19. Representative Nimbadon lavarackorum occipital regions. A in First Crania and Assessment of Species Boundaries in Nimbadon (Marsupialia: Diprotodontidae) from the Middle Miocene of Australia

Fig. 19. Representative Nimbadon lavarackorum occipital regions. A, QM F31377; B, QM F31541.

Fig. 22 in First Crania and Assessment of Species Boundaries in Nimbadon (Marsupialia: Diprotodontidae) from the Middle Miocene of Australia

Fig. 22. Variation in the Nimbadon lavarackorum mandible. A–A9, QM F53824; B–B9, QM F40337.

Fig. 12 in First Crania and Assessment of Species Boundaries in Nimbadon (Marsupialia: Diprotodontidae) from the Middle Miocene of Australia

Fig. 12 (A–H). Bivariate plots of Nimbadon lavarackorum P3 and M1 dimensions (mm) by site.

Fig. 4 in First Crania and Assessment of Species Boundaries in Nimbadon (Marsupialia: Diprotodontidae) from the Middle Miocene of Australia

Fig. 4. Right basicranium of Nimbadon lavarackorum (QM F53642).

Fig. 6 in First Crania and Assessment of Species Boundaries in Nimbadon (Marsupialia: Diprotodontidae) from the Middle Miocene of Australia

Fig. 6. Nimbadon lavarackorum occiput (QM F31377).

Fig. 3 in First Crania and Assessment of Species Boundaries in Nimbadon (Marsupialia: Diprotodontidae) from the Middle Miocene of Australia

Fig. 3. Nimbadon lavarackorum cranium (QM F50470) in: A, dorsal; B, ventral; and C, lateral views.