An official website of the United States government
Abstract The genusLiriomyzaMik (Diptera: Agromyzidae) is a diverse and globally distributed group of acalyptrate flies. Phylogenetic relationships amongLiriomyzaspecies have remained incompletely investigated and have never been fully addressed using molecular data. Here, we reconstruct the phylogeny of the genusLiriomyzausing various phylogenetic methods (maximum likelihood, Bayesian inference, and gene tree coalescence) on target‐capture‐based phylogenomic datasets (nucleotides and amino acids) obtained from anchored hybrid enrichment (AHE). We have recovered tree topologies that are nearly congruent across all data types and methods, and individual clade support is strong across all phylogenetic analyses. Moreover, defined morphological species groups and clades are well‐supported in our best estimates of the molecular phylogeny.Liriomyza violivora(Spencer) is a sister group to all remaining sampledLiriomyzaspecies, and the well‐known polyphagous vegetable pests [L. huidobrensis(Blanchard),L. langeiFrick,L. bryoniae.(Kaltenbach),L. trifolii(Burgess),L. sativaeBlanchard, andL. brassicae(Riley)]. belong to multiple clades that are not particularly closely related on the trees. Often, closely relatedLiriomyzaspecies feed on distantly related host plants. We reject the hypothesis that cophylogenetic processes betweenLiriomyzaspecies and their host plants drive diversification in this genus. Instead,Liriomyzaexhibits a widespread pattern of major host shifts across plant taxa. Our new phylogenetic estimate forLiriomyzaspecies provides considerable new information on the evolution of host‐use patterns in this genus. In addition, it provides a framework for further study of the morphology, ecology, and diversification of these important flies.
more »
« less
This content will become publicly available on January 1, 2026
Integrative taxonomy clarifies the evolution of a cryptic primate clade
Abstract Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar’s biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genusMicrocebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework.
more »
« less
- Award ID(s):
- 2148914
- PAR ID:
- 10570299
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Nature Publishing
- Date Published:
- Journal Name:
- Nature Ecology & Evolution
- Volume:
- 9
- Issue:
- 1
- ISSN:
- 2397-334X
- Page Range / eLocation ID:
- 57 to 72
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
ABSTRACT AimThuridillaBergh, 1872, is a lineage of herbivorous sea slugs externally distinguished by bright colours and distinctive patterns of lines and spots. Recent work revealed an exceptionally rapid, cryptic radiation of 13 species in the Indo‐Pacific, raising questions about mechanisms of speciation in this group. Here, we (i) study the diversification and historical biogeography ofThuridillain a phylogenetic context and (ii) assess the role of dispersal and vicariance as the predominant mode of speciation in the genus. LocationTropical and temperate regions of the Atlantic and Indo‐Pacific. Major Taxa StudiesGastropoda, Sacoglossa. MethodsA nearly complete taxon set with 28 out of 32 recognised species ofThuridillawas used, in a total sample of 172 specimens, together with sacoglossan outgroups. Phylogenetic relationships were determined using a multi‐locus approach combining two mitochondrial (COI and 16S) and one nuclear gene (H3). Species relationships, diversification times, and ancestral geographical ranges were inferred using relaxed‐clock methods together with Bayesian discrete phylogeographic methods under three calibration scenarios using the oldest known fossil of Sacoglossa,Berthelinia elegansCrosse, 1875, and tectonic events. ResultsThuridillaspecies branched off into four major clades in all calibration scenarios: two groups from the Atlantic plus Indo‐West Pacific (5 and 6 species) and two clades from the Indo‐West Pacific (4 and 17 species). The highest diversity of the genus is in the Western Pacific (14 spp.) with a peak in the East Indies Triangle (18 spp.), whereas the Atlantic is depauperate with only four species occurring in this ocean basin. Divergence between Atlantic and Indo‐West Pacific lineages occurred in two main temporal periods: the Miocene and the Pliocene. Speciation events within the 13 cryptic species‐complex fell mostly within Plio‐Pleistocene times. Main ConclusionsThe best supported hypothesis was an Indo‐West Pacific origin ofThuridillabetween 28 and 18 Mya during the Early Miocene. In the western Pacific, speciation likely occurred during transient allopatry during Plio‐Pleistocene sea‐level fluctuations. Under the three tested calibration scenarios, the limited diversity of the Atlantic Ocean is hypothesized to be derived from Miocene vicariant events associated with the closure of the Tethys Sea, dispersal across southern Africa, or long‐distance dispersal across the East Pacific Barrier prior to the uplift of the Isthmus of Panama.Thuridillais absent in the Eastern Pacific, potentially resulting from the extinction of ancestral lineages following the uplift of the Isthmus of Panama. Near‐complete sampling of diversity and reconstruction of historical biogeography thus yielded new insight into the relative contributions of dispersal versus vicariance during speciation over the history of this widely distributed, colourful genus.more » « less
-
Abstract Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population‐level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genusAptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, theAptostichus icenogleicomplex, which comprises the three sibling species,A. barackobamai,A. isabella, andA. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species‐based approach. We used genomic‐scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries withinA. icenoglei.more » « less
-
Abstract The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying the early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1,726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus—first in a widely distributed Eurasian clade and then in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also reveal several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes.more » « less
-
Abstract The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non‐lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genusCyclocosmiaAusserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework.To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North AmericanCyclocosmia,suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated viagdi, in order to avoid over splitting.more » « less
