Cladistics最新文献

Mating between species occurs within many insect orders. The result of heterospecific mating depends upon the effectiveness of pre- and post-reproductive barriers. Incomplete reproductive barriers lead to introgression of DNA into one species or both. Intricate genital morphology among dragonflies provides little assurance of species specificity given that heterospecific mating or mating attempts have been observed among many species. The genetic consequence is unknown for many heterospecific matings. For example, Somatochlora species mating and genetic exchange have been hypothesized based on observational records and individuals with hybrid morphology. We investigate the potential of heterospecific mating between North American Somatochlora species as inferred from multi-gene phylogenies. We used mitochondrial genes (COI and ND3) and nuclear genes (EF1-α and ITS2) to construct phylogenies using maximum parsimony. Observation of non-monophyletic mtDNA lineages but monophyletic nDNA lineages between Somatochlora sister-species would indicate mtDNA introgression and suggest heterospecific matings. Our results highlighted three instances of non-monophyly of mtDNA clades in the following groups: (i) S. hineana + S. tenebrosa; (ii) S. kennedyi + S. forcipata + S. franklini; and (iii) S. calverti + S. provocans + S. filosa. Analysis of partitioned Bremer support indicates that mtDNA COI largely contributed to the non-monophyly of these species, thus suggesting mtDNA introgression resulting from heterospecific matings. Additionally, the topology resulting from the combined data analysis was concordant with previous taxonomic understanding of Somatochlora species groups. These multi-gene phylogenies of North American Somatochlora are the first, providing a foundation for future ecological and evolution studies and knowledge for effective decision-making and public policy, which is especially important for the endangered species, S. hineana.

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

The Laufeia clade is a peculiar lineage of euophryine jumping spiders showing rapid divergence of male genital structures, especially the embolic complex that directly interacts with female genitalia during sperm transfer. With the rapid growth of species discovery and the perplexing morphology of male genitalia in the Laufeia clade, the controversy in its classification has become a crucial problem. In this study, we applied a phylogenomic approach using ultra-conserved elements data to infer the phylogeny of the Laufeia clade with extensive taxon sampling. A comparative morphological study was performed to evaluate diagnostic characters and understand the evolution of the male embolic complex within the Laufeia clade. The evolution of microhabitats (foliage, tree trunk, rock and surface litter) was also investigated to uncover the potential link between the microhabitat shifts and male embolic complex divergence. The results provide a strongly supported phylogenetic framework and updated generic concepts for the Laufeia clade. The synapomorphies for the updated genera within the Laufeia clade were identified through character mapping on the phylogeny. Ancestral state reconstruction analyses revealed that the Type I embolic complex (characterized by a disc-like embolic disc with a lamina as its outer edge) was ancestral and gradually evolved into the Type II (without lamina of embolic disc, base of embolic complex often modified into a functional “conductor”) and Type III (lacking lamina of embolic disc and base of embolic complex) embolic complex, and that some embolic shapes evolved multiple times independently in different lineages of the Laufeia clade. The shift from foliage-dwelling to tree trunk-dwelling in the common ancestor of the Laufeia clade may have facilitated the divergent evolution of male embolic complex in the Laufeia clade. This study provides a solid foundation for future studies of systematics and evolution of this group.

The c. 270 endemic species of Pedicularis in the Himalaya–Hengduan Mountains (HHM) region exhibit high diversity in geographic distribution, elevational range and floral morphology. Many of these, including the species with the longest corolla tubes and beaked galeas, are monophyletic and represent a putative in situ radiation. In this study, we focus on the representative Clade 3 within the HHM region. We integrate the plastid phylogeny of this clade with environmental data and species distributions to infer environmental correlates of species diversity. We estimate macroevolutionary rates and reconstructed ancestral states for geographic ranges and corolla traits, and analyse patterns of range overlap and niche evolution to assess drivers of diversification in the HHM region. Our results show that the region from northwest Yunnan to southwest Sichuan is the centre of diversity for this clade of Pedicularis. Rates of diversification are associated with precipitation and multiple environmental factors. Multiple range expansions from the Sanjiang (Three Parallel Rivers) region, followed by allopatric speciation across the HHM region, contributed to early rapid diversification. Corolla traits are not significantly associated with species diversification. This study highlights the importance of integrated evidence for understanding species diversification dynamics and contributes to our understanding of the origins of the remarkable richness of plant species in the HHM region.

The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased—80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.

Despite significant advances in alpha level taxonomy in the past few decades, the higher-level phylogeny of flat wasps (Hymenoptera, Bethylidae) remains poorly explored. Herein we provide the first phylogenomic assessment of the family based on data from ultraconserved elements for 96 species in 61 genera of the family, with material from 29 countries and all biogeographic regions. Dataset cutoffs including ultraconserved element loci recovered for 50 and 70% of terminals resulted in matrices with 1513 and 451 loci, which were analysed in both parsimony and maximum likelihood frameworks. We also provide the first analyses of divergence dating for the family based on the calibration of 12 nodes. All analyses recovered the Bethylidae as a monophyletic group and estimated the origin of the family at around 143 Ma. The results suggest that all extant subfamilies had already diversified by the Late Cretaceous. All topologies suggest that Glenosema and Chilepyris form a clade separate from other Scleroderminae; owing to the morphological distinctiveness of each genus, we propose that they are accommodated in two new subfamilies, Glenoseminae subf. nov. and Chilepyrinae subf. nov. The monotypic sclerodermine genus Galodoxa was consistently recovered within Epyrinae and is transferred to the latter subfamily.

Tooth attachment and replacement play significant roles in the feeding ecology of polyphyodont vertebrates, yet these aspects have remained largely unexplored in non-avialan paravians including troodontids. Here, we describe a new troodontid species, Urbacodon norelli sp.n., recovered from the Upper Cretaceous Iren Dabasu Formation of Inner Mongolia, China, based on an incomplete right dentary and 12 associated replacement teeth. Urbacodon norelli is distinguished from all other known troodontids, including its relative U. itemirensis from Uzbekistan, by several features: the presence of paired dentary symphyseal foramina, the presence of a relatively steep anterior margin of the dentary, the absence of a dentary chin, the presence of a common groove hosting the anterior 12 dentary teeth, and the presence of relatively larger dentary teeth. Phylogenetic analysis places both species of Urbacodon as sister taxa to Zanabazar junior, confirming their status as later-diverging troodontids. Radiographs revealed an alternating tooth replacement pattern in U. norelli, with a maximum Zahnreihen-spacing estimated to be 3. During tooth replacement, the anteriorly inclined interdental septa, which wedge between anterior dentary teeth, underwent frequent remodelling as the developing tooth moved upwards, particularly anterolabially. This rapid turnover left insufficient time for an interdental plate to form, resulting in the absence of such structures in this specimen. The frequent remodelling of periodontal tissues accompanying tooth replacement is likely to account for the absence of interdental plates. The discovery of this new troodontid expands our understanding of paravian theropods from the Upper Cretaceous Iren Dabasu Formation and provides valuable insights into troodontid tooth biology.

Here, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non-additive) symmetric, multistate linear ordered symmetric, multistate non-linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (m), maximum (g) and maximum possible (g_max) character cost for applicable character types. Algorithms for exhaustive calculation of m, g and g_max applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (m) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character g and g_max are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (g_max) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using m, g and g_max, including extra cost (h), consistency index (ci), retention index (ri) or indices based thereon.

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

Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.