Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary
Delineation of Acartia spp. is essential to assess the biodiversity of copepods in marine ecosystems. Previous phylogenetic analyses show lack of monophyly for A.tonsa and A.hudsonica. Reported average DNA sequence divergence among some Acartia spp. includes 16% for mitochondrial cytochrome oxidase...
Main Author: | |
---|---|
Other Authors: | , , |
Format: | Master Thesis |
Language: | English |
Published: |
San Francisco State University
2017
|
Subjects: | |
Online Access: | http://hdl.handle.net/10211.3/199709 |
id |
ftcalifstateuniv:oai:scholarworks:5999n496w |
---|---|
record_format |
openpolar |
spelling |
ftcalifstateuniv:oai:scholarworks:5999n496w 2024-09-30T14:40:02+00:00 Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary KeChaunte Amrie Johnson C. Sarah Cohen Wim Kimmerer Eric Routman 2017 http://hdl.handle.net/10211.3/199709 English eng San Francisco State University Science & Engineering Biology: Concentration in Integrative Biology http://hdl.handle.net/10211.3/199709 Copyright by KeChaunte Amrie Johnson, 2017 AS36 2017 BIOL .J64 Masters Thesis 2017 ftcalifstateuniv 2024-09-10T17:06:15Z Delineation of Acartia spp. is essential to assess the biodiversity of copepods in marine ecosystems. Previous phylogenetic analyses show lack of monophyly for A.tonsa and A.hudsonica. Reported average DNA sequence divergence among some Acartia spp. includes 16% for mitochondrial cytochrome oxidase c (COI) and 13%-25% for 18S rRNA. We investigated the genetic diversity of SFE Acartia in comparison to other Acartia spp. sequences from Genbank. Copepods were collected from the SFE across a range of temperatures and salinities and sequenced at COI and nuclear 18S loci for Bayesian phylogenetic comparison. We found £23% COI divergence and 35% 18S divergence among paired comparisons of A. tonsa, A. hudsonica and A. californiensis. Acartia hudsonica SFE haplotypes clustered more closely with northeast Pacific coast (-25% COI divergence) than with northeast Atlantic (-30% divergence) samples. Acartia californiensis from SFE showed 13% divergence in comparison with Genbank haplotypes. SFE and Atlantic coast A. tonsa were -15% 18S and 31-33% COI divergent. These results support high sequence divergence among Acartia species. Further analysis of additional loci is needed to understand the phylogenetic and population structure of SFE Acartia species relative to other populations. Master Thesis Northeast Atlantic Copepods Scholarworks from California State University Pacific |
institution |
Open Polar |
collection |
Scholarworks from California State University |
op_collection_id |
ftcalifstateuniv |
language |
English |
description |
Delineation of Acartia spp. is essential to assess the biodiversity of copepods in marine ecosystems. Previous phylogenetic analyses show lack of monophyly for A.tonsa and A.hudsonica. Reported average DNA sequence divergence among some Acartia spp. includes 16% for mitochondrial cytochrome oxidase c (COI) and 13%-25% for 18S rRNA. We investigated the genetic diversity of SFE Acartia in comparison to other Acartia spp. sequences from Genbank. Copepods were collected from the SFE across a range of temperatures and salinities and sequenced at COI and nuclear 18S loci for Bayesian phylogenetic comparison. We found £23% COI divergence and 35% 18S divergence among paired comparisons of A. tonsa, A. hudsonica and A. californiensis. Acartia hudsonica SFE haplotypes clustered more closely with northeast Pacific coast (-25% COI divergence) than with northeast Atlantic (-30% divergence) samples. Acartia californiensis from SFE showed 13% divergence in comparison with Genbank haplotypes. SFE and Atlantic coast A. tonsa were -15% 18S and 31-33% COI divergent. These results support high sequence divergence among Acartia species. Further analysis of additional loci is needed to understand the phylogenetic and population structure of SFE Acartia species relative to other populations. |
author2 |
C. Sarah Cohen Wim Kimmerer Eric Routman |
format |
Master Thesis |
author |
KeChaunte Amrie Johnson |
spellingShingle |
KeChaunte Amrie Johnson Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary |
author_facet |
KeChaunte Amrie Johnson |
author_sort |
KeChaunte Amrie Johnson |
title |
Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary |
title_short |
Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary |
title_full |
Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary |
title_fullStr |
Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary |
title_full_unstemmed |
Comparison of mitochondrial and nuclear genetic variation of common Acartia species in the San Francisco Estuary |
title_sort |
comparison of mitochondrial and nuclear genetic variation of common acartia species in the san francisco estuary |
publisher |
San Francisco State University |
publishDate |
2017 |
url |
http://hdl.handle.net/10211.3/199709 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Northeast Atlantic Copepods |
genre_facet |
Northeast Atlantic Copepods |
op_source |
AS36 2017 BIOL .J64 |
op_relation |
http://hdl.handle.net/10211.3/199709 |
op_rights |
Copyright by KeChaunte Amrie Johnson, 2017 |
_version_ |
1811642585686474752 |