Jinhui Shen's research while affiliated with University of Texas Southwestern Medical Center and other places
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Publications (52)
Comparative analyses of genomic data reveal further insights into the phylogeny and taxonomic classification of butterflies presented here. As a result, 2 new subgenera and 2 new species of Hesperiidae are described: Borna Grishin, subgen. n. (type species Godmania borincona Watson, 1937) and Lilla Grishin, subgen. n. (type species Choranthus lilli...
We obtained whole genome shotgun sequence reads for a number of Firetip skippers (subfamily Pyrrhopyginae), including all known species from the genera Yanguna Watson, 1893 and Gunayan Mielke, 2002 and representative species of Pyrrhopyge Hübner, [1819]. Phylogenetic analysis of their protein-coding regions unexpectedly revealed that Yanguna tetric...
The comparative genomics of butterflies yields additional insights into their phylogeny and classification that are compiled here. As a result, 3 genera, 5 subgenera, 5 species, and 3 subspecies are proposed as new, i.e., in Hesperiidae: Antina Grishin, gen. n. (type species Antigonus minor O. Mielke, 1980), Pompe Grishin and Lamas, gen. n. (type s...
The mitochondrial DNA COI barcode segment sequenced from American Anthocharis specimens across their distribution ranges partitions them into four well-separated species groups and reveals different levels of differentiation within these groups. The lanceolata group experienced the deepest divergence. About 2.7% barcode difference separates the two...
We propose a higher classification of the lycaenid hairstreak tribe Eumaeini – one of the youngest and most species‐rich butterfly tribes – based on autosome, Lepidopteran Z sex chromosome and mitochondrial protein‐coding genes. The subtribe Neolycaenina Korb is a synonym of Callophryidina Tutt and subtribe Tmolusina Bálint is a synonym of Strephon...
Our expanded efforts in genomic sequencing to cover additional skipper butterfly (Lepidoptera: Hesperiidae) species and populations, including primary type specimens, call for taxonomic changes to restore monophyly and correct misidentifications by moving taxa between genera and proposing new names. Reconciliation between phenotypic characters and...
Two new skipper butterfly (Hesperiidae) species are described from the United States: Staphylus floridus Grishin, sp. n. (type locality in Florida, Volusia Co.) and Staphylus ecos Grishin, sp. n. (type locality in Texas, Brewster Co.). They are cryptic and hence escaped recognition. They differ from their sister species by the relative size and mor...
Emesis eleanorae Gallardo & Grishin n. sp. is described from western Honduras. It differs from other species of Emesis Fabricius, 1807 in having a row of prominent iron-gray crescent-shaped postdiscal spots on both wings above, outlined by paler areas basad and mirrored as merlot-colored spots below, with the largest by the forewing costa, and in i...
Significance
Caterpillars of Eumaeus butterflies eat toxic plants and are impacted by their toxins. Despite the ancient origins of cycads, the association of cycads and Eumaeus is recent. Following a switch to feeding on cycads, Eumaeus evolved cluster egg-laying and conspicuously colored, gregarious caterpillars. Eumaeus then split into two fast e...
Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computa...
Continuing with comparative genomic exploration of worldwide butterfly fauna, we use all protein-coding genes as they are retrieved from the whole genome shotgun sequences for phylogeny construction. Analysis of these genome-scale phylogenies projected onto the taxonomic classification and the knowledge about butterfly phenotypes suggests further r...
Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen...
We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe...
Delineating species boundaries in phylogenetic groups undergoing recent radiation is a daunting challenge akin to discretizing continuity. Here, we propose a general approach exemplified by American butterflies from the genus Junonia Hübner notorious for the variety of similar phenotypes, ease of hybridization, and the lack of consensus about their...
Further genomic sequencing of butterflies by our research group expanding the coverage of species and specimens from different localities, coupled with genome-scale phylogenetic analysis and complemented by phenotypic considerations, suggests a number of changes to the names of butterflies, mostly those recorded from the United States and Canada. H...
Never before have we had the luxury of choosing a continent, picking a large phylogenetic group of animals, and obtaining genomic data for its every species. Here, we sequence all 845 species of butterflies recorded from North America north of Mexico. Our comprehensive approach reveals the pattern of diversification and adaptation occurring in this...
Genomic sequencing and analysis of worldwide skipper butterfly (Lepidoptera: Hesperiidae) fauna points to imperfections in their current classification. Some tribes, subtribes and genera as they are circumscribed today are not monophyletic. Rationalizing genomic results from the perspective of phenotypic characters suggests two new tribes, two new...
We obtained and phylogenetically analyzed whole genome shotgun sequences of nearly all species from the tribe Emesidini Seraphim, Freitas & Kaminski, 2018 (Riodinidae) and representatives from other Riodinidae tribes. We see that the recently proposed genera Neoapodemia Trujano, 2018 and Plesioarida Trujano & García, 2018 are closely allied with Ap...
Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We ded...
We obtained and analyzed whole genome data for more than 160 representatives of skipper butterflies (family Hesperiidae) from all known subfamilies, tribes and most distinctive genera. We found that two genera, Katreus Watson, 1893 and Ortholexis Karsch, 1895, which are sisters, are well-separated from all other major phylogenetic lineages and orig...
Biologists marvel at the powers of adaptive convergence, when distantly related animals look alike. While mimetic wing patterns of butterflies have fooled predators for millennia, entomologists inferred that mimics were distant relatives despite similar appearance. However, the obverse question has not been frequently asked. Who are the close relat...
For centuries, biologists have used phenotypes to infer evolution. For decades, a handful of gene markers have given us a glimpse of the genotype to combine with phenotypic traits. Today, we can sequence entire genomes from hundreds of species and gain yet closer scrutiny. To illustrate the power of genomics, we have chosen skipper butterflies (Hes...
We obtained and analyzed whole genome shotgun sequences of all 845 species of butterflies recorded from Canada and the United States. Genome-scale phylogenetic trees constructed from the data reveal several non-monophyletic genera and suggest improved classification of species included in these genera. Here, these changes are formalized and 2 subge...
Supplementary material is available on the publisher’s web site along with the published article.
Sequencing complete genomes of all major phylogenetic groups of organisms opens unprecedented opportunities to study evolution and genetics. We report draft genomes of Calephelis nemesis and Calephelis virginiensis, representatives of the family Riodinidae. They complete the genomic coverage of butterflies at the family level. At 809 and 855 Mbp, r...
Background:
The Hoary Edge Skipper (Achalarus lyciades) is an eastern North America endemic butterfly from the Eudaminae subfamily of skippers named for an underside whitish patch near the hindwing edge. Its caterpillars feed on legumes, in contrast to Grass skippers (subfamily Hesperiinae) which feed exclusively on monocots.
Results:
To better...
Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon. Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species....
Giant-Skipper butterflies from the genus Agathymus (family Hesperiidae) are unusual as their caterpillars feed inside Agave leaves. Relationships among Agathymus taxa and their names (i.e. if they are species, subspecies, or synonyms) are poorly understood due to phenotypic similarity. DNA sequences are promising to clarify the taxonomic questions,...
We assembled a complete mitochondrial genome of a unique Australian skipper butterfly Euschemon rafflesia (Hesperiidae) from next generation sequencing reads. The 15,447 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Its gene order is typical for mitogenom...
We assembled a complete mitogenome of an Asian skipper butterfly Burara striata (Hesperiidae, Coeliadinae), the first representative of the genus Burara, from next generation sequencing reads. The 15327 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T rich region. Its ge...
The Small Cabbage White ( Pieris rapae) is originally a Eurasian butterfly. Being accidentally introduced into North America, Australia, and New Zealand a century or more ago, it spread throughout the continents and rapidly established as one of the most abundant butterfly species. Although it is a serious pest of cabbage and other mustard family p...
Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729...
For 200 years zoologists have relied on phenotypes to learn about the evolution of animals. A glance at the genotype, even
through several gene markers, revolutionized our understanding of animal phylogeny. Recent advances in sequencing techniques
allow researchers to study speciation mechanisms and the link between genotype and phenotype using com...
We obtained a complete mitochondrial genome of a skipper butterfly Achalarus lyciades (Hesperiidae, Eudaminae) from next generation sequencing reads. The 15,612 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich region. Its gene order is typical for mitogenomes of Lepi...
Due to the intriguing morphology, lifecycle, and diversity of butterflies and moths, Lepidoptera are emerging as model organisms for the study of genetics, evolution and speciation. The progress of these studies relies on decoding Lepidoptera genomes, both nuclear and mitochondrial. Here we describe a protocol to obtain mitogenomes from Next Genera...
Citations
... taxonomy; classification; genomics; phylogeny; biodiversity This report is a direct continuation of our previous publications (Zhang et al. , 2020(Zhang et al. , 2021(Zhang et al. , 2022a(Zhang et al. , 2022b(Zhang et al. , 2022c, and the general philosophy employed is best summarized in the introduction to Zhang et al. (2023). Details of experimental and computational protocols are provided in the Appendix to Li et al. (2019). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/1108924942024705-1641399717430_Q64/Jing-Zhang-629.jpg)
... taxonomy; classification; genomics; phylogeny; biodiversity This report is a direct continuation of our previous publications (Zhang et al. , 2020(Zhang et al. , 2021(Zhang et al. , 2022a(Zhang et al. , 2022b(Zhang et al. , 2022c, and the general philosophy employed is best summarized in the introduction to Zhang et al. (2023). Details of experimental and computational protocols are provided in the Appendix to Li et al. (2019). ...
... In a recent paper based on analyzing molecular traits, a new higher classification for American eumaeine lycaenids was proposed (Robbins et al. 2022). Amongst the 15 subtribal names listed, there were 10 names established as new. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/626985185337344-1526496325121_Q64/Robert-Robbins-2.jpg)
... taxonomy; classification; genomics; phylogeny; biodiversity This report is a direct continuation of our previous publications (Zhang et al. , 2020(Zhang et al. , 2021(Zhang et al. , 2022a(Zhang et al. , 2022b(Zhang et al. , 2022c, and the general philosophy employed is best summarized in the introduction to Zhang et al. (2023). Details of experimental and computational protocols are provided in the Appendix to Li et al. (2019). ...
... taxonomy; classification; genomics; phylogeny; biodiversity This report is a direct continuation of our previous publications (Zhang et al. , 2020(Zhang et al. , 2021(Zhang et al. , 2022a(Zhang et al. , 2022b(Zhang et al. , 2022c, and the general philosophy employed is best summarized in the introduction to Zhang et al. (2023). Details of experimental and computational protocols are provided in the Appendix to Li et al. (2019). ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/273622447161371-1442248083868_Q64/Paul-Opler.jpg)
... taxonomy; classification; genomics; phylogeny; biodiversity This report is a direct continuation of our previous publications (Zhang et al. , 2020(Zhang et al. , 2021(Zhang et al. , 2022a(Zhang et al. , 2022b(Zhang et al. , 2022c, and the general philosophy employed is best summarized in the introduction to Zhang et al. (2023). Details of experimental and computational protocols are provided in the Appendix to Li et al. (2019). ...
... This approach generally results in a smaller number of genera, frequently due to the elimination of monotypic genera, which in our opinion, should be used only to indicate the genetic uniqueness of taxa in the absence of close relatives. Zhang et al. (2019) placed Philotiella Mattoni, [1978] (type species Lycaena speciosa Hy. Edwards, 1877) as a subgenus of Euphilotes Mattoni, [1978] (type species Lycaena enoptes Boisduval, 1852) due to their genetic similarity, as recently confirmed by Lukhtanov and Gagarina (2022). ...
... There are several recent developments that make the study of the beautiful lycaenid, the Atala Butterfly, very exciting. For instance, its life history and seasonal polyphenism have recently been examined in detail by Koi & Daniels (2017), an investigation into Atala's opsins was recently published by Liénard et al. (2021), and sequencing this species' genome helped determine some of the underlying evolutionary trends in Eumaeini (Robbins et al., 2021). The evolutionary development of the beautiful color pattern of this butterfly has not yet been studied however, and the present study is the first attempt in this direction, through the use of heparin injections. ...
... These authors anticipated that any newly discovered relatives would share more morphological characters with the type species, which caused the relationship between P. ater and P. muscorum to go unrecognized ( Fig. 4; Hutterer et al. 2018). Generating DNA sequence data from the holotype of P. ater was critical in resolving this taxonomic enigma, an approach increasingly used to resolve species limits for poorly known lineages (Kirchman et al. 2010;Kirwan et al. 2015;McGuire et al. 2018;Krabbe et al. 2020;Esselstyn et al. 2021) and groups with convoluted taxonomic histories (Chomicki and Renner 2015;Hedin et al. 2018;Contreras-Ortiz et al. 2019;Giarla and Voss 2020;Cong et al. 2021;Vences et al. 2022). We also verified the identity of the first modern specimens of P. ater following a sampling gap of 80 years since the collection of, and 55 years since the description of, the type of this species. ...
... Among the various approaches developed to recover DNA from collection specimens, hybrid enrichment methods seem to be the most efficient (Raxworthy and Smith 2021). These capture approaches can target different regions of the genome such as mitochondria (Zhang et al. 2020), exons (Bi et al. 2012), and conserved regions via conserved anchored hybrid enrichment (Espeland et al. 2018), ultraconserved elements (UCE) (Faircloth et al. 2012;Blaimer et al. 2016), and randomly distributed loci using the ddRAD approach (Suchan et al. 2016;Gauthier et al. 2020;Toussaint et al. 2021). These new methods make it possible to integrate old samples into modern genetic studies. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272753882300422-1442041001636_Q64/David-Lees-4.jpg)
